Multiple sequence alignment - TraesCS6B01G160400

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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 TraesCS6B01G160400 chr6B 100.000 4817 0 0 1 4817 164356494 164361310 0.000000e+00 8896.0
1 TraesCS6B01G160400 chr6D 96.526 2821 74 13 1608 4426 86658853 86661651 0.000000e+00 4645.0
2 TraesCS6B01G160400 chr6D 92.173 856 29 13 1 849 86656093 86656917 0.000000e+00 1175.0
3 TraesCS6B01G160400 chr6D 92.344 418 24 3 1187 1604 86658110 86658519 5.370000e-164 588.0
4 TraesCS6B01G160400 chr6D 94.030 335 11 3 852 1181 86656954 86657284 2.590000e-137 499.0
5 TraesCS6B01G160400 chr6D 87.540 313 27 5 4517 4817 86714838 86715150 7.670000e-93 351.0
6 TraesCS6B01G160400 chr6A 95.497 2909 101 19 1615 4517 104357033 104359917 0.000000e+00 4619.0
7 TraesCS6B01G160400 chr6A 95.738 2698 84 17 1615 4295 104446555 104443872 0.000000e+00 4316.0
8 TraesCS6B01G160400 chr6A 91.618 1193 42 17 3 1182 104354323 104355470 0.000000e+00 1596.0
9 TraesCS6B01G160400 chr6A 92.970 953 30 12 240 1182 104448911 104447986 0.000000e+00 1354.0
10 TraesCS6B01G160400 chr6A 96.875 352 11 0 1252 1603 104356345 104356696 1.490000e-164 590.0
11 TraesCS6B01G160400 chr6A 96.875 352 11 0 1252 1603 104447243 104446892 1.490000e-164 590.0
12 TraesCS6B01G160400 chr6A 88.636 88 10 0 4713 4800 104392529 104392616 1.830000e-19 108.0
13 TraesCS6B01G160400 chr5B 86.838 623 77 4 2621 3239 684126740 684126119 0.000000e+00 691.0
14 TraesCS6B01G160400 chr5B 86.201 587 79 2 3233 3818 684120915 684120330 6.800000e-178 634.0
15 TraesCS6B01G160400 chr5B 76.054 735 155 19 3092 3817 560442162 560441440 3.540000e-96 363.0
16 TraesCS6B01G160400 chr5B 82.633 357 57 2 1256 1611 684131552 684131200 1.300000e-80 311.0
17 TraesCS6B01G160400 chr5B 90.909 55 5 0 1127 1181 561064775 561064721 1.860000e-09 75.0
18 TraesCS6B01G160400 chr5B 90.000 50 5 0 1127 1176 560444538 560444489 1.120000e-06 65.8
19 TraesCS6B01G160400 chr4D 75.169 1035 242 15 2789 3817 15913236 15912211 1.570000e-129 473.0
20 TraesCS6B01G160400 chr4D 72.661 684 137 30 1664 2337 15914627 15913984 1.060000e-41 182.0
21 TraesCS6B01G160400 chr4A 75.024 1037 217 19 2786 3817 584679679 584680678 4.420000e-120 442.0
22 TraesCS6B01G160400 chr4A 75.048 1034 216 19 2789 3817 584735245 584734249 4.420000e-120 442.0
23 TraesCS6B01G160400 chr5A 76.269 729 158 14 3096 3818 576085595 576084876 1.640000e-99 374.0
24 TraesCS6B01G160400 chr5A 76.269 729 158 14 3096 3818 576271836 576272555 1.640000e-99 374.0
25 TraesCS6B01G160400 chr5D 75.741 742 159 19 3085 3817 458095519 458094790 2.130000e-93 353.0
26 TraesCS6B01G160400 chr5D 83.333 156 23 2 1663 1818 537224589 537224437 1.810000e-29 141.0
27 TraesCS6B01G160400 chr5D 90.000 50 5 0 1127 1176 458097945 458097896 1.120000e-06 65.8
28 TraesCS6B01G160400 chr4B 75.724 725 163 13 3098 3817 27519688 27518972 7.670000e-93 351.0
29 TraesCS6B01G160400 chr4B 73.837 688 124 28 1663 2337 27521791 27521147 6.270000e-54 222.0
30 TraesCS6B01G160400 chr4B 73.503 668 125 26 1663 2319 27249689 27250315 6.320000e-49 206.0
31 TraesCS6B01G160400 chr4B 78.210 257 52 4 2789 3043 27520220 27519966 1.390000e-35 161.0


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 TraesCS6B01G160400 chr6B 164356494 164361310 4816 False 8896.000000 8896 100.000000 1 4817 1 chr6B.!!$F1 4816
1 TraesCS6B01G160400 chr6D 86656093 86661651 5558 False 1726.750000 4645 93.768250 1 4426 4 chr6D.!!$F2 4425
2 TraesCS6B01G160400 chr6A 104354323 104359917 5594 False 2268.333333 4619 94.663333 3 4517 3 chr6A.!!$F2 4514
3 TraesCS6B01G160400 chr6A 104443872 104448911 5039 True 2086.666667 4316 95.194333 240 4295 3 chr6A.!!$R1 4055
4 TraesCS6B01G160400 chr5B 684126119 684126740 621 True 691.000000 691 86.838000 2621 3239 1 chr5B.!!$R3 618
5 TraesCS6B01G160400 chr5B 684120330 684120915 585 True 634.000000 634 86.201000 3233 3818 1 chr5B.!!$R2 585
6 TraesCS6B01G160400 chr5B 560441440 560444538 3098 True 214.400000 363 83.027000 1127 3817 2 chr5B.!!$R5 2690
7 TraesCS6B01G160400 chr4D 15912211 15914627 2416 True 327.500000 473 73.915000 1664 3817 2 chr4D.!!$R1 2153
8 TraesCS6B01G160400 chr4A 584679679 584680678 999 False 442.000000 442 75.024000 2786 3817 1 chr4A.!!$F1 1031
9 TraesCS6B01G160400 chr4A 584734249 584735245 996 True 442.000000 442 75.048000 2789 3817 1 chr4A.!!$R1 1028
10 TraesCS6B01G160400 chr5A 576084876 576085595 719 True 374.000000 374 76.269000 3096 3818 1 chr5A.!!$R1 722
11 TraesCS6B01G160400 chr5A 576271836 576272555 719 False 374.000000 374 76.269000 3096 3818 1 chr5A.!!$F1 722
12 TraesCS6B01G160400 chr5D 458094790 458097945 3155 True 209.400000 353 82.870500 1127 3817 2 chr5D.!!$R2 2690
13 TraesCS6B01G160400 chr4B 27518972 27521791 2819 True 244.666667 351 75.923667 1663 3817 3 chr4B.!!$R1 2154
14 TraesCS6B01G160400 chr4B 27249689 27250315 626 False 206.000000 206 73.503000 1663 2319 1 chr4B.!!$F1 656

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
348 361 0.031994 GAATGCGCCGGCCATTTATT 59.968 50.000 30.95 20.38 38.85 1.40 F
669 691 0.296349 CGCACATGCATGCAAATTCG 59.704 50.000 26.68 20.68 46.47 3.34 F
921 982 0.389817 CGTGAGCTTCATCGTCCCAA 60.390 55.000 0.00 0.00 0.00 4.12 F
1182 1243 1.282157 GACCCCAGTAAGCAACATCCT 59.718 52.381 0.00 0.00 0.00 3.24 F
1833 3188 0.462047 GCGATCCGGACCACAAGAAT 60.462 55.000 6.12 0.00 0.00 2.40 F
2568 4431 0.743701 CGCTGCTCTTCCTGCAAGAT 60.744 55.000 0.00 0.00 40.55 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1309 2327 0.179018 GGAGCACCCAGTGTTCAACT 60.179 55.000 12.63 0.0 43.74 3.16 R
1605 2629 0.396139 ATTGTTCATGGCCCGATGCT 60.396 50.000 0.00 0.0 40.92 3.79 R
1821 3176 0.744771 GGCGAGGATTCTTGTGGTCC 60.745 60.000 0.00 0.0 0.00 4.46 R
2739 4605 2.024868 CCACGCGGAATCGTTCACA 61.025 57.895 12.47 0.0 41.21 3.58 R
3351 5611 1.898574 CTGGCCAAAGTTGACGGCT 60.899 57.895 7.01 0.0 45.50 5.52 R
4463 6741 0.403271 ACTTGCTGCATGGGAAGACT 59.597 50.000 18.21 0.0 37.92 3.24 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
102 104 7.024340 AGAAAAATGATCAATGGTCTCATCG 57.976 36.000 0.00 0.00 32.24 3.84
137 140 5.432885 ACATAGTTTTTGTCACCTTTCCG 57.567 39.130 0.00 0.00 0.00 4.30
140 143 1.407618 GTTTTTGTCACCTTTCCGCCT 59.592 47.619 0.00 0.00 0.00 5.52
182 185 7.534239 GTCTCTGGTAAAAATACTTTTTCTGCG 59.466 37.037 1.15 0.00 41.60 5.18
197 200 1.679311 TGCGGAGAAGCCACAGAAT 59.321 52.632 0.00 0.00 35.94 2.40
265 274 5.029014 CGAAGTCAATAGTACAAGTCGAGG 58.971 45.833 0.00 0.00 0.00 4.63
345 358 4.191950 CGAATGCGCCGGCCATTT 62.192 61.111 30.95 19.41 38.85 2.32
346 359 2.829206 CGAATGCGCCGGCCATTTA 61.829 57.895 30.95 13.15 38.85 1.40
347 360 1.659794 GAATGCGCCGGCCATTTAT 59.340 52.632 30.95 17.79 38.85 1.40
348 361 0.031994 GAATGCGCCGGCCATTTATT 59.968 50.000 30.95 20.38 38.85 1.40
365 378 2.126914 ATTAGACAGCGATGACGAGC 57.873 50.000 8.12 0.00 42.66 5.03
391 404 1.781429 CGAGTAGCATGCACGTACATC 59.219 52.381 21.98 11.35 0.00 3.06
397 410 1.398041 GCATGCACGTACATCACATGT 59.602 47.619 14.21 0.00 46.92 3.21
398 411 2.607180 GCATGCACGTACATCACATGTA 59.393 45.455 14.21 0.00 44.38 2.29
463 483 2.110188 TCCCGAGCCTTATCTCCTGTAT 59.890 50.000 0.00 0.00 0.00 2.29
464 484 2.232452 CCCGAGCCTTATCTCCTGTATG 59.768 54.545 0.00 0.00 0.00 2.39
465 485 2.894126 CCGAGCCTTATCTCCTGTATGT 59.106 50.000 0.00 0.00 0.00 2.29
466 486 4.079970 CCGAGCCTTATCTCCTGTATGTA 58.920 47.826 0.00 0.00 0.00 2.29
616 638 1.594293 CAACTCCGTCGCCTTGTGT 60.594 57.895 0.00 0.00 0.00 3.72
617 639 1.594293 AACTCCGTCGCCTTGTGTG 60.594 57.895 0.00 0.00 0.00 3.82
655 677 2.925594 ATGTACACACATGCGCACA 58.074 47.368 14.90 3.29 43.89 4.57
656 678 1.452110 ATGTACACACATGCGCACAT 58.548 45.000 14.90 6.08 43.89 3.21
669 691 0.296349 CGCACATGCATGCAAATTCG 59.704 50.000 26.68 20.68 46.47 3.34
835 857 0.606604 AGAACGACGGCAACCATAGT 59.393 50.000 0.00 0.00 0.00 2.12
912 973 1.758440 AAGGGCACTCGTGAGCTTCA 61.758 55.000 6.84 0.00 0.00 3.02
921 982 0.389817 CGTGAGCTTCATCGTCCCAA 60.390 55.000 0.00 0.00 0.00 4.12
922 983 1.808411 GTGAGCTTCATCGTCCCAAA 58.192 50.000 0.00 0.00 0.00 3.28
923 984 2.359900 GTGAGCTTCATCGTCCCAAAT 58.640 47.619 0.00 0.00 0.00 2.32
924 985 2.352960 GTGAGCTTCATCGTCCCAAATC 59.647 50.000 0.00 0.00 0.00 2.17
1005 1066 2.672478 CGAGAGCGTGAGGAAGATGTTT 60.672 50.000 0.00 0.00 0.00 2.83
1182 1243 1.282157 GACCCCAGTAAGCAACATCCT 59.718 52.381 0.00 0.00 0.00 3.24
1183 1244 1.710809 ACCCCAGTAAGCAACATCCTT 59.289 47.619 0.00 0.00 0.00 3.36
1184 1245 2.290960 ACCCCAGTAAGCAACATCCTTC 60.291 50.000 0.00 0.00 0.00 3.46
1185 1246 2.025887 CCCCAGTAAGCAACATCCTTCT 60.026 50.000 0.00 0.00 0.00 2.85
1209 2133 9.368416 TCTCTTCATTTATGTATGGCTAGTAGT 57.632 33.333 0.00 0.00 0.00 2.73
1218 2142 3.648683 ATGGCTAGTAGTAATCCCCCA 57.351 47.619 0.00 0.00 0.00 4.96
1223 2147 4.449131 GCTAGTAGTAATCCCCCACAAAC 58.551 47.826 0.00 0.00 0.00 2.93
1227 2151 3.434940 AGTAATCCCCCACAAACTGAC 57.565 47.619 0.00 0.00 0.00 3.51
1239 2163 4.515191 CCACAAACTGACTAAGCAAGCTAA 59.485 41.667 0.00 0.00 0.00 3.09
1240 2164 5.182001 CCACAAACTGACTAAGCAAGCTAAT 59.818 40.000 0.00 0.00 0.00 1.73
1244 2168 6.674694 AACTGACTAAGCAAGCTAATGATG 57.325 37.500 0.00 0.00 0.00 3.07
1246 2170 5.104776 ACTGACTAAGCAAGCTAATGATGGA 60.105 40.000 0.00 0.00 0.00 3.41
1249 2173 6.261603 TGACTAAGCAAGCTAATGATGGAATG 59.738 38.462 0.00 0.00 0.00 2.67
1613 2968 3.854666 CTGGACATATTCTAGCATCGGG 58.145 50.000 0.00 0.00 0.00 5.14
1627 2982 2.287788 GCATCGGGCCATGAACAATTAG 60.288 50.000 16.83 0.00 36.11 1.73
1647 3002 6.598753 TTAGTAAGTGAACTGAACAAGCAC 57.401 37.500 0.00 0.00 0.00 4.40
1648 3003 3.555956 AGTAAGTGAACTGAACAAGCACG 59.444 43.478 0.00 0.00 34.82 5.34
1649 3004 2.309528 AGTGAACTGAACAAGCACGA 57.690 45.000 0.00 0.00 34.82 4.35
1650 3005 2.838736 AGTGAACTGAACAAGCACGAT 58.161 42.857 0.00 0.00 34.82 3.73
1654 3009 3.814842 TGAACTGAACAAGCACGATTGAT 59.185 39.130 1.43 0.00 34.20 2.57
1659 3014 3.065233 TGAACAAGCACGATTGATATGCC 59.935 43.478 1.43 0.00 40.33 4.40
1833 3188 0.462047 GCGATCCGGACCACAAGAAT 60.462 55.000 6.12 0.00 0.00 2.40
2568 4431 0.743701 CGCTGCTCTTCCTGCAAGAT 60.744 55.000 0.00 0.00 40.55 2.40
2860 4859 1.687612 CACCCCATCCACAAGCTCT 59.312 57.895 0.00 0.00 0.00 4.09
3384 5644 0.744874 GCCAGTACTCATACGCAGGA 59.255 55.000 0.00 0.00 36.33 3.86
3828 6088 4.814147 TCTCCATCTGATCGATGTTATGC 58.186 43.478 19.28 0.00 46.56 3.14
3831 6091 3.320626 CATCTGATCGATGTTATGCCGT 58.679 45.455 0.54 0.00 43.66 5.68
3832 6092 3.452755 TCTGATCGATGTTATGCCGTT 57.547 42.857 0.54 0.00 0.00 4.44
3850 6110 8.627487 ATGCCGTTTTATGTTATTGTTGTATG 57.373 30.769 0.00 0.00 0.00 2.39
3944 6204 4.141855 AGGCGAGTTGTGTTTATTTTCG 57.858 40.909 0.00 0.00 0.00 3.46
4154 6426 1.795768 TTGCTGATGTCGACCACTTC 58.204 50.000 14.12 5.59 0.00 3.01
4283 6555 3.973206 TTTTCTTCGGAGATGGTAGCA 57.027 42.857 0.00 0.00 35.04 3.49
4284 6556 3.973206 TTTCTTCGGAGATGGTAGCAA 57.027 42.857 0.00 0.00 35.04 3.91
4296 6570 7.052873 GGAGATGGTAGCAATGCTCATATTAT 58.947 38.462 12.53 0.00 40.44 1.28
4368 6646 8.673711 GTGTGATATTTTTGTCCATGCTAGTTA 58.326 33.333 0.00 0.00 0.00 2.24
4467 6745 3.874392 GCACATGCCCAATTTTAGTCT 57.126 42.857 0.00 0.00 34.31 3.24
4468 6746 4.192429 GCACATGCCCAATTTTAGTCTT 57.808 40.909 0.00 0.00 34.31 3.01
4469 6747 4.176271 GCACATGCCCAATTTTAGTCTTC 58.824 43.478 0.00 0.00 34.31 2.87
4470 6748 4.747810 CACATGCCCAATTTTAGTCTTCC 58.252 43.478 0.00 0.00 0.00 3.46
4471 6749 3.769300 ACATGCCCAATTTTAGTCTTCCC 59.231 43.478 0.00 0.00 0.00 3.97
4479 6757 2.877097 TTTAGTCTTCCCATGCAGCA 57.123 45.000 0.00 0.00 0.00 4.41
4490 6768 3.055963 TCCCATGCAGCAAGTTTTAATGG 60.056 43.478 0.00 0.00 34.21 3.16
4517 6796 3.620488 TCCCATACAGGAACAAAGATGC 58.380 45.455 0.00 0.00 41.22 3.91
4518 6797 2.689983 CCCATACAGGAACAAAGATGCC 59.310 50.000 0.00 0.00 41.22 4.40
4519 6798 3.624777 CCATACAGGAACAAAGATGCCT 58.375 45.455 0.00 0.00 41.22 4.75
4520 6799 3.629398 CCATACAGGAACAAAGATGCCTC 59.371 47.826 0.00 0.00 41.22 4.70
4521 6800 4.521146 CATACAGGAACAAAGATGCCTCT 58.479 43.478 0.00 0.00 0.00 3.69
4522 6801 2.787994 ACAGGAACAAAGATGCCTCTG 58.212 47.619 0.00 0.00 0.00 3.35
4523 6802 2.089980 CAGGAACAAAGATGCCTCTGG 58.910 52.381 0.00 0.00 0.00 3.86
4556 6835 1.613836 GGCCAGGCCTAGATGAAATG 58.386 55.000 24.99 0.00 46.69 2.32
4557 6836 0.957362 GCCAGGCCTAGATGAAATGC 59.043 55.000 3.98 0.00 0.00 3.56
4558 6837 1.478288 GCCAGGCCTAGATGAAATGCT 60.478 52.381 3.98 0.00 0.00 3.79
4559 6838 2.228059 CCAGGCCTAGATGAAATGCTG 58.772 52.381 3.98 0.00 0.00 4.41
4560 6839 2.228059 CAGGCCTAGATGAAATGCTGG 58.772 52.381 3.98 0.00 0.00 4.85
4561 6840 0.957362 GGCCTAGATGAAATGCTGGC 59.043 55.000 0.00 0.00 38.28 4.85
4562 6841 0.590195 GCCTAGATGAAATGCTGGCG 59.410 55.000 0.00 0.00 0.00 5.69
4563 6842 1.233019 CCTAGATGAAATGCTGGCGG 58.767 55.000 0.00 0.00 0.00 6.13
4564 6843 0.590195 CTAGATGAAATGCTGGCGGC 59.410 55.000 12.43 12.43 42.22 6.53
4618 6897 3.838795 GCGACGGCAGCGTGTTAG 61.839 66.667 0.00 0.00 39.62 2.34
4619 6898 3.179265 CGACGGCAGCGTGTTAGG 61.179 66.667 0.00 0.00 0.00 2.69
4620 6899 3.488090 GACGGCAGCGTGTTAGGC 61.488 66.667 0.00 0.00 0.00 3.93
4623 6902 3.488090 GGCAGCGTGTTAGGCGTC 61.488 66.667 0.00 0.00 33.62 5.19
4624 6903 3.838795 GCAGCGTGTTAGGCGTCG 61.839 66.667 0.00 0.00 33.62 5.12
4625 6904 2.126618 CAGCGTGTTAGGCGTCGA 60.127 61.111 0.00 0.00 33.62 4.20
4626 6905 2.152699 CAGCGTGTTAGGCGTCGAG 61.153 63.158 0.00 0.00 33.62 4.04
4627 6906 2.879462 GCGTGTTAGGCGTCGAGG 60.879 66.667 0.00 0.00 0.00 4.63
4628 6907 2.564975 CGTGTTAGGCGTCGAGGT 59.435 61.111 7.01 0.00 0.00 3.85
4629 6908 1.800315 CGTGTTAGGCGTCGAGGTG 60.800 63.158 7.01 0.00 0.00 4.00
4630 6909 1.445582 GTGTTAGGCGTCGAGGTGG 60.446 63.158 7.01 0.00 0.00 4.61
4631 6910 1.904865 TGTTAGGCGTCGAGGTGGT 60.905 57.895 7.01 0.00 0.00 4.16
4632 6911 1.445582 GTTAGGCGTCGAGGTGGTG 60.446 63.158 7.01 0.00 0.00 4.17
4633 6912 1.904865 TTAGGCGTCGAGGTGGTGT 60.905 57.895 7.01 0.00 0.00 4.16
4634 6913 2.149803 TTAGGCGTCGAGGTGGTGTG 62.150 60.000 7.01 0.00 0.00 3.82
4637 6916 3.991051 CGTCGAGGTGGTGTGCCT 61.991 66.667 0.00 0.00 39.42 4.75
4638 6917 2.357517 GTCGAGGTGGTGTGCCTG 60.358 66.667 0.00 0.00 36.29 4.85
4639 6918 4.314440 TCGAGGTGGTGTGCCTGC 62.314 66.667 0.00 0.00 36.29 4.85
4640 6919 4.320456 CGAGGTGGTGTGCCTGCT 62.320 66.667 0.00 0.00 36.29 4.24
4641 6920 2.670934 GAGGTGGTGTGCCTGCTG 60.671 66.667 0.00 0.00 36.29 4.41
4642 6921 4.275508 AGGTGGTGTGCCTGCTGG 62.276 66.667 5.03 5.03 34.56 4.85
4653 6932 4.335647 CTGCTGGGCGGTTGAGGT 62.336 66.667 0.00 0.00 0.00 3.85
4654 6933 4.329545 TGCTGGGCGGTTGAGGTC 62.330 66.667 0.00 0.00 0.00 3.85
4662 6941 3.766691 GGTTGAGGTCGCCGGCTA 61.767 66.667 26.68 11.79 0.00 3.93
4663 6942 2.202756 GTTGAGGTCGCCGGCTAG 60.203 66.667 26.68 10.37 0.00 3.42
4664 6943 2.361992 TTGAGGTCGCCGGCTAGA 60.362 61.111 26.68 13.00 0.00 2.43
4665 6944 2.415608 TTGAGGTCGCCGGCTAGAG 61.416 63.158 26.68 9.07 0.00 2.43
4666 6945 4.273257 GAGGTCGCCGGCTAGAGC 62.273 72.222 26.68 23.65 41.14 4.09
4668 6947 4.577246 GGTCGCCGGCTAGAGCAG 62.577 72.222 26.68 6.92 44.36 4.24
4669 6948 3.518998 GTCGCCGGCTAGAGCAGA 61.519 66.667 26.68 9.61 44.36 4.26
4670 6949 2.519541 TCGCCGGCTAGAGCAGAT 60.520 61.111 26.68 0.00 44.36 2.90
4671 6950 2.355599 CGCCGGCTAGAGCAGATG 60.356 66.667 26.68 0.00 44.36 2.90
4672 6951 2.030262 GCCGGCTAGAGCAGATGG 59.970 66.667 22.15 0.85 44.36 3.51
4673 6952 2.739784 CCGGCTAGAGCAGATGGG 59.260 66.667 3.54 0.00 44.36 4.00
4674 6953 2.030262 CGGCTAGAGCAGATGGGC 59.970 66.667 3.54 0.00 44.36 5.36
4675 6954 2.429494 GGCTAGAGCAGATGGGCC 59.571 66.667 3.54 0.00 44.36 5.80
4676 6955 2.446848 GGCTAGAGCAGATGGGCCA 61.447 63.158 9.61 9.61 44.36 5.36
4677 6956 1.528824 GCTAGAGCAGATGGGCCAA 59.471 57.895 11.89 0.00 41.59 4.52
4678 6957 0.110104 GCTAGAGCAGATGGGCCAAT 59.890 55.000 11.89 0.00 41.59 3.16
4679 6958 1.881498 GCTAGAGCAGATGGGCCAATC 60.881 57.143 11.89 12.77 41.59 2.67
4680 6959 1.698532 CTAGAGCAGATGGGCCAATCT 59.301 52.381 17.73 17.73 37.39 2.40
4681 6960 1.811778 AGAGCAGATGGGCCAATCTA 58.188 50.000 22.84 0.00 35.09 1.98
4682 6961 1.698532 AGAGCAGATGGGCCAATCTAG 59.301 52.381 22.84 16.87 35.09 2.43
4683 6962 0.110104 AGCAGATGGGCCAATCTAGC 59.890 55.000 22.84 24.48 35.09 3.42
4689 6968 2.505982 GGCCAATCTAGCCGCTCA 59.494 61.111 0.00 0.00 41.41 4.26
4690 6969 1.153168 GGCCAATCTAGCCGCTCAA 60.153 57.895 0.00 0.00 41.41 3.02
4691 6970 1.162800 GGCCAATCTAGCCGCTCAAG 61.163 60.000 0.00 0.00 41.41 3.02
4692 6971 1.780025 GCCAATCTAGCCGCTCAAGC 61.780 60.000 0.00 0.00 37.78 4.01
4703 6982 4.069232 CTCAAGCGAGCGGGGTGA 62.069 66.667 0.00 0.00 31.00 4.02
4704 6983 4.373116 TCAAGCGAGCGGGGTGAC 62.373 66.667 0.00 0.00 0.00 3.67
4757 7036 3.450115 GCCGTCGGCTAGTGGAGT 61.450 66.667 28.98 0.00 46.69 3.85
4758 7037 3.003113 GCCGTCGGCTAGTGGAGTT 62.003 63.158 28.98 0.00 46.69 3.01
4759 7038 1.660560 GCCGTCGGCTAGTGGAGTTA 61.661 60.000 28.98 0.00 46.69 2.24
4760 7039 0.813184 CCGTCGGCTAGTGGAGTTAA 59.187 55.000 0.00 0.00 0.00 2.01
4761 7040 1.468736 CCGTCGGCTAGTGGAGTTAAC 60.469 57.143 0.00 0.00 0.00 2.01
4762 7041 1.792993 CGTCGGCTAGTGGAGTTAACG 60.793 57.143 0.00 0.00 0.00 3.18
4763 7042 0.813184 TCGGCTAGTGGAGTTAACGG 59.187 55.000 0.00 0.00 0.00 4.44
4764 7043 0.804933 CGGCTAGTGGAGTTAACGGC 60.805 60.000 0.00 0.00 0.00 5.68
4765 7044 0.248289 GGCTAGTGGAGTTAACGGCA 59.752 55.000 0.00 0.00 0.00 5.69
4766 7045 1.134491 GGCTAGTGGAGTTAACGGCAT 60.134 52.381 0.00 0.00 0.00 4.40
4767 7046 1.933853 GCTAGTGGAGTTAACGGCATG 59.066 52.381 0.00 0.00 0.00 4.06
4768 7047 2.550978 CTAGTGGAGTTAACGGCATGG 58.449 52.381 0.00 0.00 0.00 3.66
4769 7048 0.676782 AGTGGAGTTAACGGCATGGC 60.677 55.000 9.69 9.69 0.00 4.40
4770 7049 0.676782 GTGGAGTTAACGGCATGGCT 60.677 55.000 18.09 1.58 0.00 4.75
4771 7050 0.676466 TGGAGTTAACGGCATGGCTG 60.676 55.000 18.09 13.01 41.29 4.85
4772 7051 1.376609 GGAGTTAACGGCATGGCTGG 61.377 60.000 18.09 5.11 39.57 4.85
4773 7052 0.392461 GAGTTAACGGCATGGCTGGA 60.392 55.000 18.09 0.00 39.57 3.86
4774 7053 0.255890 AGTTAACGGCATGGCTGGAT 59.744 50.000 18.09 7.18 39.57 3.41
4775 7054 0.663153 GTTAACGGCATGGCTGGATC 59.337 55.000 18.09 1.57 39.57 3.36
4776 7055 0.465460 TTAACGGCATGGCTGGATCC 60.465 55.000 18.09 4.20 39.57 3.36
4777 7056 2.658679 TAACGGCATGGCTGGATCCG 62.659 60.000 18.09 10.72 45.04 4.18
4784 7063 4.467084 GGCTGGATCCGCCACGAA 62.467 66.667 30.59 4.39 46.77 3.85
4785 7064 2.435938 GCTGGATCCGCCACGAAA 60.436 61.111 15.14 0.00 43.33 3.46
4786 7065 2.038269 GCTGGATCCGCCACGAAAA 61.038 57.895 15.14 0.00 43.33 2.29
4787 7066 1.376609 GCTGGATCCGCCACGAAAAT 61.377 55.000 15.14 0.00 43.33 1.82
4788 7067 0.657840 CTGGATCCGCCACGAAAATC 59.342 55.000 7.39 0.00 43.33 2.17
4789 7068 0.251916 TGGATCCGCCACGAAAATCT 59.748 50.000 7.39 0.00 43.33 2.40
4790 7069 0.938008 GGATCCGCCACGAAAATCTC 59.062 55.000 0.00 0.00 36.34 2.75
4791 7070 1.651987 GATCCGCCACGAAAATCTCA 58.348 50.000 0.00 0.00 0.00 3.27
4792 7071 1.327764 GATCCGCCACGAAAATCTCAC 59.672 52.381 0.00 0.00 0.00 3.51
4793 7072 0.034198 TCCGCCACGAAAATCTCACA 59.966 50.000 0.00 0.00 0.00 3.58
4794 7073 1.086696 CCGCCACGAAAATCTCACAT 58.913 50.000 0.00 0.00 0.00 3.21
4795 7074 1.202065 CCGCCACGAAAATCTCACATG 60.202 52.381 0.00 0.00 0.00 3.21
4796 7075 1.731709 CGCCACGAAAATCTCACATGA 59.268 47.619 0.00 0.00 0.00 3.07
4797 7076 2.352651 CGCCACGAAAATCTCACATGAT 59.647 45.455 0.00 0.00 0.00 2.45
4798 7077 3.181507 CGCCACGAAAATCTCACATGATT 60.182 43.478 0.00 0.00 38.19 2.57
4799 7078 4.672542 CGCCACGAAAATCTCACATGATTT 60.673 41.667 0.00 0.00 45.32 2.17
4800 7079 4.560035 GCCACGAAAATCTCACATGATTTG 59.440 41.667 0.00 0.00 43.40 2.32
4801 7080 4.560035 CCACGAAAATCTCACATGATTTGC 59.440 41.667 0.00 1.47 43.40 3.68
4802 7081 4.560035 CACGAAAATCTCACATGATTTGCC 59.440 41.667 0.00 0.08 43.40 4.52
4803 7082 4.107622 CGAAAATCTCACATGATTTGCCC 58.892 43.478 0.00 0.00 43.40 5.36
4804 7083 4.436332 GAAAATCTCACATGATTTGCCCC 58.564 43.478 0.00 0.00 43.40 5.80
4805 7084 1.683943 ATCTCACATGATTTGCCCCG 58.316 50.000 0.00 0.00 0.00 5.73
4806 7085 1.031571 TCTCACATGATTTGCCCCGC 61.032 55.000 0.00 0.00 0.00 6.13
4807 7086 1.303970 TCACATGATTTGCCCCGCA 60.304 52.632 0.00 0.00 36.47 5.69
4808 7087 1.153784 CACATGATTTGCCCCGCAC 60.154 57.895 0.00 0.00 38.71 5.34
4809 7088 1.606025 ACATGATTTGCCCCGCACA 60.606 52.632 0.00 0.00 38.71 4.57
4810 7089 1.184322 ACATGATTTGCCCCGCACAA 61.184 50.000 0.00 0.00 38.71 3.33
4811 7090 0.176219 CATGATTTGCCCCGCACAAT 59.824 50.000 0.00 0.00 38.71 2.71
4812 7091 0.903942 ATGATTTGCCCCGCACAATT 59.096 45.000 0.00 0.00 38.71 2.32
4813 7092 0.037512 TGATTTGCCCCGCACAATTG 60.038 50.000 3.24 3.24 38.71 2.32
4814 7093 0.037419 GATTTGCCCCGCACAATTGT 60.037 50.000 4.92 4.92 38.71 2.71
4815 7094 0.396060 ATTTGCCCCGCACAATTGTT 59.604 45.000 8.77 0.00 38.71 2.83
4816 7095 0.179000 TTTGCCCCGCACAATTGTTT 59.821 45.000 8.77 0.00 38.71 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.338674 TGATTTGCGATCAGTTCCGGT 60.339 47.619 0.00 0.00 0.00 5.28
10 11 3.469899 TTTGATTTGCGATCAGTTCCG 57.530 42.857 3.25 0.00 0.00 4.30
102 104 8.474006 ACAAAAACTATGTTTTCTGTGGAAAC 57.526 30.769 8.57 0.00 40.63 2.78
182 185 9.875691 AATTAATTTTTATTCTGTGGCTTCTCC 57.124 29.630 0.00 0.00 0.00 3.71
197 200 9.651913 CAAGGCTCCAGCTAAAATTAATTTTTA 57.348 29.630 26.56 14.03 37.69 1.52
345 358 2.616842 TGCTCGTCATCGCTGTCTAATA 59.383 45.455 0.00 0.00 36.96 0.98
346 359 1.405463 TGCTCGTCATCGCTGTCTAAT 59.595 47.619 0.00 0.00 36.96 1.73
347 360 0.808755 TGCTCGTCATCGCTGTCTAA 59.191 50.000 0.00 0.00 36.96 2.10
348 361 0.378610 CTGCTCGTCATCGCTGTCTA 59.621 55.000 0.00 0.00 36.96 2.59
365 378 1.517039 TGCATGCTACTCGACGCTG 60.517 57.895 20.33 0.00 0.00 5.18
391 404 8.939929 GGAGAACCATACATTGATATACATGTG 58.060 37.037 9.11 0.00 35.97 3.21
397 410 7.455953 AGAGCAGGAGAACCATACATTGATATA 59.544 37.037 0.00 0.00 38.94 0.86
398 411 6.271857 AGAGCAGGAGAACCATACATTGATAT 59.728 38.462 0.00 0.00 38.94 1.63
463 483 1.097232 CAGGACCGGACGTACATACA 58.903 55.000 9.46 0.00 0.00 2.29
464 484 0.248784 GCAGGACCGGACGTACATAC 60.249 60.000 9.46 0.00 0.00 2.39
465 485 1.717791 CGCAGGACCGGACGTACATA 61.718 60.000 9.46 0.00 0.00 2.29
466 486 2.890371 GCAGGACCGGACGTACAT 59.110 61.111 9.46 0.00 0.00 2.29
535 555 0.531200 AAGTACGTAGTCCTGCCAGC 59.469 55.000 2.79 0.00 43.93 4.85
563 585 3.853671 CCACCGTACGTACACTGTTTATC 59.146 47.826 24.50 0.00 0.00 1.75
616 638 7.914427 ACATGGTAGACCTATTAAGTGATCA 57.086 36.000 0.00 0.00 36.82 2.92
617 639 8.857098 TGTACATGGTAGACCTATTAAGTGATC 58.143 37.037 0.00 0.00 36.82 2.92
669 691 1.134461 TGCCATGCAAATAACCCATGC 60.134 47.619 0.00 0.00 40.45 4.06
912 973 1.474077 GCTTGCTTGATTTGGGACGAT 59.526 47.619 0.00 0.00 0.00 3.73
921 982 0.037605 GGCTGCTTGCTTGCTTGATT 60.038 50.000 0.00 0.00 42.39 2.57
922 983 0.898789 AGGCTGCTTGCTTGCTTGAT 60.899 50.000 0.00 0.00 42.39 2.57
923 984 1.529948 AGGCTGCTTGCTTGCTTGA 60.530 52.632 0.00 0.00 42.39 3.02
924 985 1.372997 CAGGCTGCTTGCTTGCTTG 60.373 57.895 0.00 8.99 41.75 4.01
984 1045 0.453793 ACATCTTCCTCACGCTCTCG 59.546 55.000 0.00 0.00 42.43 4.04
1183 1244 9.368416 ACTACTAGCCATACATAAATGAAGAGA 57.632 33.333 0.00 0.00 0.00 3.10
1200 2124 2.686119 TGTGGGGGATTACTACTAGCC 58.314 52.381 0.00 0.00 0.00 3.93
1208 2132 3.434940 AGTCAGTTTGTGGGGGATTAC 57.565 47.619 0.00 0.00 0.00 1.89
1209 2133 4.566907 GCTTAGTCAGTTTGTGGGGGATTA 60.567 45.833 0.00 0.00 0.00 1.75
1210 2134 3.814316 GCTTAGTCAGTTTGTGGGGGATT 60.814 47.826 0.00 0.00 0.00 3.01
1211 2135 2.290960 GCTTAGTCAGTTTGTGGGGGAT 60.291 50.000 0.00 0.00 0.00 3.85
1212 2136 1.073284 GCTTAGTCAGTTTGTGGGGGA 59.927 52.381 0.00 0.00 0.00 4.81
1218 2142 5.997746 TCATTAGCTTGCTTAGTCAGTTTGT 59.002 36.000 0.00 0.00 0.00 2.83
1223 2147 5.363101 TCCATCATTAGCTTGCTTAGTCAG 58.637 41.667 0.00 0.00 0.00 3.51
1227 2151 5.564259 GCCATTCCATCATTAGCTTGCTTAG 60.564 44.000 0.00 0.00 0.00 2.18
1239 2163 2.111077 TCCATCCATGCCATTCCATCAT 59.889 45.455 0.00 0.00 0.00 2.45
1240 2164 1.499870 TCCATCCATGCCATTCCATCA 59.500 47.619 0.00 0.00 0.00 3.07
1244 2168 0.606604 GCATCCATCCATGCCATTCC 59.393 55.000 0.00 0.00 43.03 3.01
1309 2327 0.179018 GGAGCACCCAGTGTTCAACT 60.179 55.000 12.63 0.00 43.74 3.16
1418 2442 0.390735 GTGGCGTGGTAGTTCCGAAT 60.391 55.000 0.00 0.00 39.52 3.34
1495 2519 1.792367 CATGAGTTTGCGACGAAGACA 59.208 47.619 0.00 0.00 0.00 3.41
1605 2629 0.396139 ATTGTTCATGGCCCGATGCT 60.396 50.000 0.00 0.00 40.92 3.79
1613 2968 7.023575 CAGTTCACTTACTAATTGTTCATGGC 58.976 38.462 0.00 0.00 0.00 4.40
1627 2982 3.554324 TCGTGCTTGTTCAGTTCACTTAC 59.446 43.478 0.00 0.00 0.00 2.34
1647 3002 2.159747 CGTCTGCATGGCATATCAATCG 60.160 50.000 0.00 5.54 38.13 3.34
1648 3003 2.810274 ACGTCTGCATGGCATATCAATC 59.190 45.455 0.00 0.00 38.13 2.67
1649 3004 2.854963 ACGTCTGCATGGCATATCAAT 58.145 42.857 0.00 0.00 38.13 2.57
1650 3005 2.330440 ACGTCTGCATGGCATATCAA 57.670 45.000 0.00 0.00 38.13 2.57
1654 3009 1.119684 AGGTACGTCTGCATGGCATA 58.880 50.000 0.00 0.00 38.13 3.14
1821 3176 0.744771 GGCGAGGATTCTTGTGGTCC 60.745 60.000 0.00 0.00 0.00 4.46
2274 3732 3.278592 GGCGAACTCCTCGTCCGTT 62.279 63.158 0.00 0.00 46.75 4.44
2568 4431 2.343758 GGCTTGAGAGTGCCGTCA 59.656 61.111 0.00 0.00 39.71 4.35
2739 4605 2.024868 CCACGCGGAATCGTTCACA 61.025 57.895 12.47 0.00 41.21 3.58
2860 4859 2.668212 GCGGTAGTGTGGCTGCAA 60.668 61.111 0.50 0.00 37.00 4.08
3351 5611 1.898574 CTGGCCAAAGTTGACGGCT 60.899 57.895 7.01 0.00 45.50 5.52
3384 5644 2.062177 CGGACGGTTGGGGAGGTAT 61.062 63.158 0.00 0.00 0.00 2.73
3850 6110 4.625311 CGTTCCTTATTTGCAATGGGAAAC 59.375 41.667 18.00 10.72 37.15 2.78
3889 6149 1.078918 CGCTTCTGGCCACTCATGA 60.079 57.895 0.00 0.00 37.74 3.07
3944 6204 3.555547 GGCCAAAACAACTTCATCAACAC 59.444 43.478 0.00 0.00 0.00 3.32
4231 6503 6.799926 AAAATTATGGTTGCCATGAACAAC 57.200 33.333 18.15 18.15 44.84 3.32
4271 6543 2.627515 TGAGCATTGCTACCATCTCC 57.372 50.000 11.96 0.00 39.88 3.71
4274 6546 9.565213 GAAAATAATATGAGCATTGCTACCATC 57.435 33.333 11.96 0.00 39.88 3.51
4275 6547 8.526147 GGAAAATAATATGAGCATTGCTACCAT 58.474 33.333 11.96 13.79 39.88 3.55
4276 6548 7.725397 AGGAAAATAATATGAGCATTGCTACCA 59.275 33.333 11.96 6.83 39.88 3.25
4277 6549 8.115490 AGGAAAATAATATGAGCATTGCTACC 57.885 34.615 11.96 0.32 39.88 3.18
4279 6551 9.578576 AGAAGGAAAATAATATGAGCATTGCTA 57.421 29.630 11.96 0.00 39.88 3.49
4280 6552 8.474710 AGAAGGAAAATAATATGAGCATTGCT 57.525 30.769 11.79 11.79 43.88 3.91
4281 6553 9.189723 GAAGAAGGAAAATAATATGAGCATTGC 57.810 33.333 0.00 0.00 0.00 3.56
4282 6554 9.390795 CGAAGAAGGAAAATAATATGAGCATTG 57.609 33.333 0.00 0.00 0.00 2.82
4283 6555 8.571336 CCGAAGAAGGAAAATAATATGAGCATT 58.429 33.333 0.00 0.00 0.00 3.56
4284 6556 7.721399 ACCGAAGAAGGAAAATAATATGAGCAT 59.279 33.333 0.00 0.00 34.73 3.79
4296 6570 2.946990 GTGGTGAACCGAAGAAGGAAAA 59.053 45.455 0.00 0.00 39.43 2.29
4319 6593 7.148086 ACACGCAAAATCATAATACCATGAAGT 60.148 33.333 0.00 0.00 38.39 3.01
4340 6618 3.547468 GCATGGACAAAAATATCACACGC 59.453 43.478 0.00 0.00 0.00 5.34
4426 6704 7.725251 TGTGCCAAGATTAGACTTTCAAAAAT 58.275 30.769 0.00 0.00 0.00 1.82
4429 6707 6.680810 CATGTGCCAAGATTAGACTTTCAAA 58.319 36.000 0.00 0.00 0.00 2.69
4430 6708 5.335897 GCATGTGCCAAGATTAGACTTTCAA 60.336 40.000 0.00 0.00 34.31 2.69
4431 6709 4.156556 GCATGTGCCAAGATTAGACTTTCA 59.843 41.667 0.00 0.00 34.31 2.69
4432 6710 4.666237 GCATGTGCCAAGATTAGACTTTC 58.334 43.478 0.00 0.00 34.31 2.62
4433 6711 4.708726 GCATGTGCCAAGATTAGACTTT 57.291 40.909 0.00 0.00 34.31 2.66
4462 6740 1.630369 ACTTGCTGCATGGGAAGACTA 59.370 47.619 18.21 0.00 37.92 2.59
4463 6741 0.403271 ACTTGCTGCATGGGAAGACT 59.597 50.000 18.21 0.00 37.92 3.24
4464 6742 1.251251 AACTTGCTGCATGGGAAGAC 58.749 50.000 18.21 0.00 37.92 3.01
4465 6743 1.999648 AAACTTGCTGCATGGGAAGA 58.000 45.000 18.21 0.00 37.92 2.87
4466 6744 2.825861 AAAACTTGCTGCATGGGAAG 57.174 45.000 18.21 8.40 39.88 3.46
4467 6745 4.563168 CCATTAAAACTTGCTGCATGGGAA 60.563 41.667 18.21 7.90 0.00 3.97
4468 6746 3.055963 CCATTAAAACTTGCTGCATGGGA 60.056 43.478 18.21 0.00 0.00 4.37
4469 6747 3.264104 CCATTAAAACTTGCTGCATGGG 58.736 45.455 18.21 8.07 0.00 4.00
4470 6748 3.264104 CCCATTAAAACTTGCTGCATGG 58.736 45.455 18.21 12.84 0.00 3.66
4471 6749 2.674357 GCCCATTAAAACTTGCTGCATG 59.326 45.455 13.31 13.31 0.00 4.06
4490 6768 0.470341 GTTCCTGTATGGGAGGAGCC 59.530 60.000 0.00 0.00 40.79 4.70
4502 6781 2.553904 CCAGAGGCATCTTTGTTCCTGT 60.554 50.000 0.00 0.00 31.64 4.00
4503 6782 2.089980 CCAGAGGCATCTTTGTTCCTG 58.910 52.381 0.00 0.00 31.64 3.86
4538 6817 0.957362 GCATTTCATCTAGGCCTGGC 59.043 55.000 17.99 11.05 0.00 4.85
4539 6818 2.228059 CAGCATTTCATCTAGGCCTGG 58.772 52.381 17.99 14.14 0.00 4.45
4540 6819 2.228059 CCAGCATTTCATCTAGGCCTG 58.772 52.381 17.99 5.60 0.00 4.85
4541 6820 1.478288 GCCAGCATTTCATCTAGGCCT 60.478 52.381 11.78 11.78 34.71 5.19
4542 6821 0.957362 GCCAGCATTTCATCTAGGCC 59.043 55.000 0.00 0.00 34.71 5.19
4543 6822 0.590195 CGCCAGCATTTCATCTAGGC 59.410 55.000 0.00 0.00 37.32 3.93
4544 6823 1.233019 CCGCCAGCATTTCATCTAGG 58.767 55.000 0.00 0.00 0.00 3.02
4545 6824 0.590195 GCCGCCAGCATTTCATCTAG 59.410 55.000 0.00 0.00 42.97 2.43
4546 6825 2.706636 GCCGCCAGCATTTCATCTA 58.293 52.632 0.00 0.00 42.97 1.98
4547 6826 3.518003 GCCGCCAGCATTTCATCT 58.482 55.556 0.00 0.00 42.97 2.90
4601 6880 3.838795 CTAACACGCTGCCGTCGC 61.839 66.667 0.00 0.00 46.39 5.19
4602 6881 3.179265 CCTAACACGCTGCCGTCG 61.179 66.667 0.00 0.00 46.39 5.12
4603 6882 3.488090 GCCTAACACGCTGCCGTC 61.488 66.667 0.00 0.00 46.39 4.79
4606 6885 3.488090 GACGCCTAACACGCTGCC 61.488 66.667 0.00 0.00 0.00 4.85
4607 6886 3.838795 CGACGCCTAACACGCTGC 61.839 66.667 0.00 0.00 0.00 5.25
4608 6887 2.126618 TCGACGCCTAACACGCTG 60.127 61.111 0.00 0.00 0.00 5.18
4609 6888 2.178521 CTCGACGCCTAACACGCT 59.821 61.111 0.00 0.00 0.00 5.07
4610 6889 2.879462 CCTCGACGCCTAACACGC 60.879 66.667 0.00 0.00 0.00 5.34
4611 6890 1.800315 CACCTCGACGCCTAACACG 60.800 63.158 0.00 0.00 0.00 4.49
4612 6891 1.445582 CCACCTCGACGCCTAACAC 60.446 63.158 0.00 0.00 0.00 3.32
4613 6892 1.904865 ACCACCTCGACGCCTAACA 60.905 57.895 0.00 0.00 0.00 2.41
4614 6893 1.445582 CACCACCTCGACGCCTAAC 60.446 63.158 0.00 0.00 0.00 2.34
4615 6894 1.904865 ACACCACCTCGACGCCTAA 60.905 57.895 0.00 0.00 0.00 2.69
4616 6895 2.282674 ACACCACCTCGACGCCTA 60.283 61.111 0.00 0.00 0.00 3.93
4617 6896 3.991051 CACACCACCTCGACGCCT 61.991 66.667 0.00 0.00 0.00 5.52
4620 6899 3.991051 AGGCACACCACCTCGACG 61.991 66.667 0.00 0.00 39.06 5.12
4621 6900 2.357517 CAGGCACACCACCTCGAC 60.358 66.667 0.00 0.00 39.06 4.20
4622 6901 4.314440 GCAGGCACACCACCTCGA 62.314 66.667 0.00 0.00 39.06 4.04
4623 6902 4.320456 AGCAGGCACACCACCTCG 62.320 66.667 0.00 0.00 39.06 4.63
4624 6903 2.670934 CAGCAGGCACACCACCTC 60.671 66.667 0.00 0.00 39.06 3.85
4625 6904 4.275508 CCAGCAGGCACACCACCT 62.276 66.667 0.00 0.00 39.06 4.00
4636 6915 4.335647 ACCTCAACCGCCCAGCAG 62.336 66.667 0.00 0.00 0.00 4.24
4637 6916 4.329545 GACCTCAACCGCCCAGCA 62.330 66.667 0.00 0.00 0.00 4.41
4645 6924 3.718210 CTAGCCGGCGACCTCAACC 62.718 68.421 23.20 0.00 0.00 3.77
4646 6925 2.202756 CTAGCCGGCGACCTCAAC 60.203 66.667 23.20 0.00 0.00 3.18
4647 6926 2.361992 TCTAGCCGGCGACCTCAA 60.362 61.111 23.20 0.19 0.00 3.02
4648 6927 2.829003 CTCTAGCCGGCGACCTCA 60.829 66.667 23.20 1.84 0.00 3.86
4649 6928 4.273257 GCTCTAGCCGGCGACCTC 62.273 72.222 23.20 8.10 34.31 3.85
4651 6930 4.577246 CTGCTCTAGCCGGCGACC 62.577 72.222 23.20 9.69 41.18 4.79
4652 6931 2.851071 ATCTGCTCTAGCCGGCGAC 61.851 63.158 23.20 10.52 41.18 5.19
4653 6932 2.519541 ATCTGCTCTAGCCGGCGA 60.520 61.111 23.20 16.40 41.18 5.54
4654 6933 2.355599 CATCTGCTCTAGCCGGCG 60.356 66.667 23.20 8.11 41.18 6.46
4655 6934 2.030262 CCATCTGCTCTAGCCGGC 59.970 66.667 21.89 21.89 41.18 6.13
4656 6935 2.739784 CCCATCTGCTCTAGCCGG 59.260 66.667 0.00 0.00 41.18 6.13
4657 6936 2.030262 GCCCATCTGCTCTAGCCG 59.970 66.667 0.00 0.00 41.18 5.52
4658 6937 1.987807 TTGGCCCATCTGCTCTAGCC 61.988 60.000 0.00 0.00 41.18 3.93
4659 6938 0.110104 ATTGGCCCATCTGCTCTAGC 59.890 55.000 0.00 0.00 42.50 3.42
4660 6939 1.698532 AGATTGGCCCATCTGCTCTAG 59.301 52.381 18.26 0.00 0.00 2.43
4661 6940 1.811778 AGATTGGCCCATCTGCTCTA 58.188 50.000 18.26 0.00 0.00 2.43
4662 6941 1.698532 CTAGATTGGCCCATCTGCTCT 59.301 52.381 25.87 5.91 0.00 4.09
4663 6942 1.881498 GCTAGATTGGCCCATCTGCTC 60.881 57.143 25.87 12.60 0.00 4.26
4664 6943 0.110104 GCTAGATTGGCCCATCTGCT 59.890 55.000 25.87 6.00 0.00 4.24
4665 6944 0.892814 GGCTAGATTGGCCCATCTGC 60.893 60.000 25.87 23.79 43.49 4.26
4666 6945 0.604780 CGGCTAGATTGGCCCATCTG 60.605 60.000 25.87 17.20 46.24 2.90
4667 6946 1.757306 CGGCTAGATTGGCCCATCT 59.243 57.895 22.06 22.06 46.24 2.90
4668 6947 1.968540 GCGGCTAGATTGGCCCATC 60.969 63.158 8.81 8.81 46.24 3.51
4669 6948 2.113986 GCGGCTAGATTGGCCCAT 59.886 61.111 0.00 0.00 46.24 4.00
4670 6949 3.089874 AGCGGCTAGATTGGCCCA 61.090 61.111 0.00 0.00 46.24 5.36
4671 6950 2.281139 GAGCGGCTAGATTGGCCC 60.281 66.667 0.60 0.00 46.24 5.80
4672 6951 1.153168 TTGAGCGGCTAGATTGGCC 60.153 57.895 0.60 0.00 45.57 5.36
4673 6952 1.780025 GCTTGAGCGGCTAGATTGGC 61.780 60.000 0.60 0.00 0.00 4.52
4674 6953 2.315246 GCTTGAGCGGCTAGATTGG 58.685 57.895 0.60 0.00 0.00 3.16
4686 6965 4.069232 TCACCCCGCTCGCTTGAG 62.069 66.667 0.00 0.00 42.93 3.02
4687 6966 4.373116 GTCACCCCGCTCGCTTGA 62.373 66.667 0.00 0.00 0.00 3.02
4741 7020 0.813184 TTAACTCCACTAGCCGACGG 59.187 55.000 10.29 10.29 0.00 4.79
4742 7021 1.792993 CGTTAACTCCACTAGCCGACG 60.793 57.143 3.71 0.00 0.00 5.12
4743 7022 1.468736 CCGTTAACTCCACTAGCCGAC 60.469 57.143 3.71 0.00 0.00 4.79
4744 7023 0.813184 CCGTTAACTCCACTAGCCGA 59.187 55.000 3.71 0.00 0.00 5.54
4745 7024 0.804933 GCCGTTAACTCCACTAGCCG 60.805 60.000 3.71 0.00 0.00 5.52
4746 7025 0.248289 TGCCGTTAACTCCACTAGCC 59.752 55.000 3.71 0.00 0.00 3.93
4747 7026 1.933853 CATGCCGTTAACTCCACTAGC 59.066 52.381 3.71 0.00 0.00 3.42
4748 7027 2.550978 CCATGCCGTTAACTCCACTAG 58.449 52.381 3.71 0.00 0.00 2.57
4749 7028 1.406341 GCCATGCCGTTAACTCCACTA 60.406 52.381 3.71 0.00 0.00 2.74
4750 7029 0.676782 GCCATGCCGTTAACTCCACT 60.677 55.000 3.71 0.00 0.00 4.00
4751 7030 0.676782 AGCCATGCCGTTAACTCCAC 60.677 55.000 3.71 0.00 0.00 4.02
4752 7031 0.676466 CAGCCATGCCGTTAACTCCA 60.676 55.000 3.71 0.88 0.00 3.86
4753 7032 1.376609 CCAGCCATGCCGTTAACTCC 61.377 60.000 3.71 0.00 0.00 3.85
4754 7033 0.392461 TCCAGCCATGCCGTTAACTC 60.392 55.000 3.71 0.00 0.00 3.01
4755 7034 0.255890 ATCCAGCCATGCCGTTAACT 59.744 50.000 3.71 0.00 0.00 2.24
4756 7035 0.663153 GATCCAGCCATGCCGTTAAC 59.337 55.000 0.00 0.00 0.00 2.01
4757 7036 0.465460 GGATCCAGCCATGCCGTTAA 60.465 55.000 6.95 0.00 0.00 2.01
4758 7037 1.148273 GGATCCAGCCATGCCGTTA 59.852 57.895 6.95 0.00 0.00 3.18
4759 7038 2.124151 GGATCCAGCCATGCCGTT 60.124 61.111 6.95 0.00 0.00 4.44
4760 7039 4.552365 CGGATCCAGCCATGCCGT 62.552 66.667 13.41 0.00 37.35 5.68
4770 7049 0.251916 AGATTTTCGTGGCGGATCCA 59.748 50.000 13.41 0.00 44.18 3.41
4771 7050 0.938008 GAGATTTTCGTGGCGGATCC 59.062 55.000 0.00 0.00 0.00 3.36
4772 7051 1.327764 GTGAGATTTTCGTGGCGGATC 59.672 52.381 0.00 0.00 0.00 3.36
4773 7052 1.338674 TGTGAGATTTTCGTGGCGGAT 60.339 47.619 0.00 0.00 0.00 4.18
4774 7053 0.034198 TGTGAGATTTTCGTGGCGGA 59.966 50.000 0.00 0.00 0.00 5.54
4775 7054 1.086696 ATGTGAGATTTTCGTGGCGG 58.913 50.000 0.00 0.00 0.00 6.13
4776 7055 1.731709 TCATGTGAGATTTTCGTGGCG 59.268 47.619 0.00 0.00 0.00 5.69
4777 7056 4.361451 AATCATGTGAGATTTTCGTGGC 57.639 40.909 0.00 0.00 34.70 5.01
4778 7057 4.560035 GCAAATCATGTGAGATTTTCGTGG 59.440 41.667 0.00 0.00 43.67 4.94
4779 7058 4.560035 GGCAAATCATGTGAGATTTTCGTG 59.440 41.667 0.00 0.00 43.67 4.35
4780 7059 4.380867 GGGCAAATCATGTGAGATTTTCGT 60.381 41.667 0.00 0.00 43.67 3.85
4781 7060 4.107622 GGGCAAATCATGTGAGATTTTCG 58.892 43.478 0.00 0.00 43.67 3.46
4782 7061 4.436332 GGGGCAAATCATGTGAGATTTTC 58.564 43.478 0.00 0.00 43.67 2.29
4783 7062 3.119029 CGGGGCAAATCATGTGAGATTTT 60.119 43.478 0.00 0.00 43.67 1.82
4784 7063 2.428171 CGGGGCAAATCATGTGAGATTT 59.572 45.455 0.00 0.00 46.23 2.17
4785 7064 2.026641 CGGGGCAAATCATGTGAGATT 58.973 47.619 0.00 0.00 39.81 2.40
4786 7065 1.683943 CGGGGCAAATCATGTGAGAT 58.316 50.000 0.00 0.00 0.00 2.75
4787 7066 1.031571 GCGGGGCAAATCATGTGAGA 61.032 55.000 0.00 0.00 0.00 3.27
4788 7067 1.314534 TGCGGGGCAAATCATGTGAG 61.315 55.000 0.00 0.00 34.76 3.51
4789 7068 1.303970 TGCGGGGCAAATCATGTGA 60.304 52.632 0.00 0.00 34.76 3.58
4790 7069 1.153784 GTGCGGGGCAAATCATGTG 60.154 57.895 0.00 0.00 41.47 3.21
4791 7070 1.184322 TTGTGCGGGGCAAATCATGT 61.184 50.000 0.00 0.00 41.47 3.21
4792 7071 0.176219 ATTGTGCGGGGCAAATCATG 59.824 50.000 0.00 0.00 41.47 3.07
4793 7072 0.903942 AATTGTGCGGGGCAAATCAT 59.096 45.000 0.00 0.00 41.47 2.45
4794 7073 0.037512 CAATTGTGCGGGGCAAATCA 60.038 50.000 0.00 0.00 41.47 2.57
4795 7074 0.037419 ACAATTGTGCGGGGCAAATC 60.037 50.000 11.07 0.00 41.47 2.17
4796 7075 0.396060 AACAATTGTGCGGGGCAAAT 59.604 45.000 12.82 0.00 41.47 2.32
4797 7076 0.179000 AAACAATTGTGCGGGGCAAA 59.821 45.000 12.82 0.00 41.47 3.68
4798 7077 1.826024 AAACAATTGTGCGGGGCAA 59.174 47.368 12.82 0.00 41.47 4.52
4799 7078 3.543537 AAACAATTGTGCGGGGCA 58.456 50.000 12.82 0.00 35.60 5.36


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

AutoCloner maintained by Alex Coulton.