Multiple sequence alignment - TraesCS6D01G327000

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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 TraesCS6D01G327000 chr6D 100.000 9509 0 0 1 9509 431923301 431932809 0.000000e+00 17560.0
1 TraesCS6D01G327000 chr6D 97.561 41 1 0 9465 9505 408657441 408657481 4.760000e-08 71.3
2 TraesCS6D01G327000 chr6D 97.368 38 1 0 9466 9503 118271789 118271752 2.220000e-06 65.8
3 TraesCS6D01G327000 chr6D 97.297 37 1 0 9469 9505 355155762 355155726 7.970000e-06 63.9
4 TraesCS6D01G327000 chrUn 96.203 4530 123 23 1188 5699 74606962 74611460 0.000000e+00 7367.0
5 TraesCS6D01G327000 chrUn 97.592 2948 63 6 5698 8643 74611565 74614506 0.000000e+00 5044.0
6 TraesCS6D01G327000 chrUn 91.296 540 20 10 8935 9463 74614789 74615312 0.000000e+00 712.0
7 TraesCS6D01G327000 chrUn 90.909 220 13 4 8724 8940 74614541 74614756 1.210000e-73 289.0
8 TraesCS6D01G327000 chrUn 83.548 310 38 6 791 1095 74605996 74606297 2.620000e-70 278.0
9 TraesCS6D01G327000 chr6B 91.677 4085 237 53 2777 6818 651996420 652000444 0.000000e+00 5565.0
10 TraesCS6D01G327000 chr6B 94.065 2241 101 9 6815 9030 652001287 652003520 0.000000e+00 3373.0
11 TraesCS6D01G327000 chr6B 95.077 1747 83 3 6782 8526 652063189 652064934 0.000000e+00 2747.0
12 TraesCS6D01G327000 chr6B 84.785 1722 157 54 919 2572 651994646 651996330 0.000000e+00 1631.0
13 TraesCS6D01G327000 chr6B 86.776 673 62 15 62 719 592965166 592964506 0.000000e+00 725.0
14 TraesCS6D01G327000 chr6B 86.923 520 42 19 226 721 720202641 720202124 2.320000e-155 560.0
15 TraesCS6D01G327000 chr6B 87.305 449 36 6 8542 8971 652122059 652122505 2.390000e-135 494.0
16 TraesCS6D01G327000 chr6B 88.462 364 38 3 5257 5617 652150671 652151033 4.080000e-118 436.0
17 TraesCS6D01G327000 chr6B 89.139 267 17 5 9077 9332 652016480 652016745 1.190000e-83 322.0
18 TraesCS6D01G327000 chr6B 94.118 102 4 2 1 101 592965298 592965198 4.600000e-33 154.0
19 TraesCS6D01G327000 chr6B 89.623 106 4 3 9358 9463 652016744 652016842 2.790000e-25 128.0
20 TraesCS6D01G327000 chr6B 91.111 90 3 2 9073 9162 652123143 652123227 6.030000e-22 117.0
21 TraesCS6D01G327000 chr6B 92.982 57 4 0 791 847 651994508 651994564 6.120000e-12 84.2
22 TraesCS6D01G327000 chr6B 95.745 47 2 0 8858 8904 646261926 646261972 1.020000e-09 76.8
23 TraesCS6D01G327000 chr5A 90.013 751 40 17 3 723 484592787 484592042 0.000000e+00 939.0
24 TraesCS6D01G327000 chr3D 91.766 668 36 10 63 719 610705518 610704859 0.000000e+00 911.0
25 TraesCS6D01G327000 chr3D 89.603 731 46 15 1 716 537586749 537587464 0.000000e+00 902.0
26 TraesCS6D01G327000 chr3D 90.669 568 25 12 1 543 55374441 55373877 0.000000e+00 730.0
27 TraesCS6D01G327000 chr3D 97.222 36 1 0 8869 8904 598084789 598084824 2.870000e-05 62.1
28 TraesCS6D01G327000 chr4A 89.310 739 40 17 1 719 510648353 510647634 0.000000e+00 891.0
29 TraesCS6D01G327000 chr4A 90.385 52 2 1 9454 9505 668081606 668081654 2.220000e-06 65.8
30 TraesCS6D01G327000 chr6A 88.785 749 45 14 1 718 569588290 569589030 0.000000e+00 881.0
31 TraesCS6D01G327000 chr3A 88.740 746 50 15 1 719 80407393 80408131 0.000000e+00 881.0
32 TraesCS6D01G327000 chr2A 88.251 749 54 18 1 721 378393369 378394111 0.000000e+00 865.0
33 TraesCS6D01G327000 chr2A 83.660 765 65 17 1 719 266630039 266630789 0.000000e+00 665.0
34 TraesCS6D01G327000 chr5D 89.911 674 41 12 62 721 57136461 57135801 0.000000e+00 843.0
35 TraesCS6D01G327000 chr5D 97.561 41 1 0 9466 9506 456614082 456614122 4.760000e-08 71.3
36 TraesCS6D01G327000 chr5D 97.500 40 1 0 9466 9505 428835343 428835304 1.710000e-07 69.4
37 TraesCS6D01G327000 chr5D 100.000 31 0 0 8875 8905 411630969 411630999 3.710000e-04 58.4
38 TraesCS6D01G327000 chr5D 89.362 47 2 3 8878 8923 506089394 506089350 1.000000e-03 56.5
39 TraesCS6D01G327000 chr4D 91.800 561 32 8 1 551 285409695 285410251 0.000000e+00 769.0
40 TraesCS6D01G327000 chr4D 97.561 41 1 0 9465 9505 75227629 75227669 4.760000e-08 71.3
41 TraesCS6D01G327000 chr4D 97.561 41 1 0 9465 9505 453259833 453259793 4.760000e-08 71.3
42 TraesCS6D01G327000 chr4D 95.122 41 2 0 9465 9505 324685408 324685448 2.220000e-06 65.8
43 TraesCS6D01G327000 chr4D 97.368 38 1 0 9468 9505 484620636 484620599 2.220000e-06 65.8
44 TraesCS6D01G327000 chr7A 84.820 751 58 20 1 721 18858824 18858100 0.000000e+00 704.0
45 TraesCS6D01G327000 chr1D 89.474 475 26 9 252 715 96103991 96104452 6.400000e-161 579.0
46 TraesCS6D01G327000 chr1D 86.503 163 7 5 1 148 96103491 96103653 2.120000e-36 165.0
47 TraesCS6D01G327000 chr1D 97.561 41 1 0 9465 9505 144940377 144940417 4.760000e-08 71.3
48 TraesCS6D01G327000 chr1D 97.500 40 1 0 9466 9505 144940776 144940737 1.710000e-07 69.4
49 TraesCS6D01G327000 chr1D 97.500 40 1 0 9466 9505 227859672 227859711 1.710000e-07 69.4
50 TraesCS6D01G327000 chr7D 89.933 298 13 6 1 281 475990149 475990446 1.510000e-97 368.0
51 TraesCS6D01G327000 chr7D 93.878 49 3 0 8858 8906 512118590 512118542 3.680000e-09 75.0
52 TraesCS6D01G327000 chr5B 95.745 47 2 0 8858 8904 39738084 39738130 1.020000e-09 76.8
53 TraesCS6D01G327000 chr4B 97.561 41 1 0 9465 9505 51741000 51740960 4.760000e-08 71.3
54 TraesCS6D01G327000 chr4B 95.122 41 2 0 9465 9505 457769320 457769360 2.220000e-06 65.8
55 TraesCS6D01G327000 chr3B 95.349 43 2 0 9463 9505 661839602 661839644 1.710000e-07 69.4
56 TraesCS6D01G327000 chr2B 95.349 43 2 0 9463 9505 208621762 208621804 1.710000e-07 69.4
57 TraesCS6D01G327000 chr2D 97.368 38 0 1 8875 8912 179329085 179329121 7.970000e-06 63.9
58 TraesCS6D01G327000 chr1B 90.698 43 4 0 8863 8905 188263499 188263541 3.710000e-04 58.4
59 TraesCS6D01G327000 chr1B 92.500 40 2 1 8875 8914 95662240 95662278 1.000000e-03 56.5


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 TraesCS6D01G327000 chr6D 431923301 431932809 9508 False 17560.0 17560 100.00000 1 9509 1 chr6D.!!$F2 9508
1 TraesCS6D01G327000 chrUn 74605996 74615312 9316 False 2738.0 7367 91.90960 791 9463 5 chrUn.!!$F1 8672
2 TraesCS6D01G327000 chr6B 652063189 652064934 1745 False 2747.0 2747 95.07700 6782 8526 1 chr6B.!!$F2 1744
3 TraesCS6D01G327000 chr6B 651994508 652003520 9012 False 2663.3 5565 90.87725 791 9030 4 chr6B.!!$F4 8239
4 TraesCS6D01G327000 chr6B 720202124 720202641 517 True 560.0 560 86.92300 226 721 1 chr6B.!!$R1 495
5 TraesCS6D01G327000 chr6B 592964506 592965298 792 True 439.5 725 90.44700 1 719 2 chr6B.!!$R2 718
6 TraesCS6D01G327000 chr6B 652122059 652123227 1168 False 305.5 494 89.20800 8542 9162 2 chr6B.!!$F6 620
7 TraesCS6D01G327000 chr5A 484592042 484592787 745 True 939.0 939 90.01300 3 723 1 chr5A.!!$R1 720
8 TraesCS6D01G327000 chr3D 610704859 610705518 659 True 911.0 911 91.76600 63 719 1 chr3D.!!$R2 656
9 TraesCS6D01G327000 chr3D 537586749 537587464 715 False 902.0 902 89.60300 1 716 1 chr3D.!!$F1 715
10 TraesCS6D01G327000 chr3D 55373877 55374441 564 True 730.0 730 90.66900 1 543 1 chr3D.!!$R1 542
11 TraesCS6D01G327000 chr4A 510647634 510648353 719 True 891.0 891 89.31000 1 719 1 chr4A.!!$R1 718
12 TraesCS6D01G327000 chr6A 569588290 569589030 740 False 881.0 881 88.78500 1 718 1 chr6A.!!$F1 717
13 TraesCS6D01G327000 chr3A 80407393 80408131 738 False 881.0 881 88.74000 1 719 1 chr3A.!!$F1 718
14 TraesCS6D01G327000 chr2A 378393369 378394111 742 False 865.0 865 88.25100 1 721 1 chr2A.!!$F2 720
15 TraesCS6D01G327000 chr2A 266630039 266630789 750 False 665.0 665 83.66000 1 719 1 chr2A.!!$F1 718
16 TraesCS6D01G327000 chr5D 57135801 57136461 660 True 843.0 843 89.91100 62 721 1 chr5D.!!$R1 659
17 TraesCS6D01G327000 chr4D 285409695 285410251 556 False 769.0 769 91.80000 1 551 1 chr4D.!!$F2 550
18 TraesCS6D01G327000 chr7A 18858100 18858824 724 True 704.0 704 84.82000 1 721 1 chr7A.!!$R1 720
19 TraesCS6D01G327000 chr1D 96103491 96104452 961 False 372.0 579 87.98850 1 715 2 chr1D.!!$F3 714

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
723 1093 0.029567 CCACTAGACGCGTCCATCTC 59.970 60.000 34.08 10.65 0.00 2.75 F
882 1286 0.610687 CAAGGCTCTCTCGTTCCCTT 59.389 55.000 0.00 0.00 36.38 3.95 F
1558 2561 0.615331 CTCTTGGCTGGGACTTAGCA 59.385 55.000 0.00 0.00 42.88 3.49 F
2372 3407 0.337428 AGGGCCTCTTTGGAATGCAT 59.663 50.000 0.00 0.00 38.35 3.96 F
2373 3408 1.570501 AGGGCCTCTTTGGAATGCATA 59.429 47.619 0.00 0.00 38.35 3.14 F
2726 3768 1.611673 GGATAATGGATCACCTGGCGG 60.612 57.143 0.00 0.00 36.12 6.13 F
2747 3789 3.181523 GGTAGCCGAACTTCGAAAATGAC 60.182 47.826 12.87 2.33 43.74 3.06 F
4763 5817 0.843309 TGCCTTCTGTCCTTGTTCCA 59.157 50.000 0.00 0.00 0.00 3.53 F
6208 7390 0.877743 GCTCCTTCCTGAACAAGTGC 59.122 55.000 0.00 0.00 0.00 4.40 F
6991 9028 1.002468 ACTGCGAAACATGTTGAGCAC 60.002 47.619 27.09 11.86 34.06 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1541 2544 0.326264 ACTGCTAAGTCCCAGCCAAG 59.674 55.000 0.00 0.00 38.29 3.61 R
1768 2788 0.389037 CTCAGCAGCGCTAACTGTCA 60.389 55.000 28.72 16.13 36.40 3.58 R
2667 3709 0.682209 CCAGCTCTTCCCATGGGTTG 60.682 60.000 30.28 22.32 36.47 3.77 R
4322 5376 3.898482 AGACAAAAGGTAGGCAACAGTT 58.102 40.909 0.00 0.00 41.41 3.16 R
4431 5485 5.940470 GCTAGTTCTTTTTCCAGAGGATTGA 59.060 40.000 0.00 0.00 0.00 2.57 R
4763 5817 5.449553 AGACCACAAGAAGAAGATGGTTTT 58.550 37.500 0.00 0.00 43.73 2.43 R
4877 5932 7.855904 CACTTGGCCAAATAATTAGTTACGATC 59.144 37.037 20.91 0.00 0.00 3.69 R
6771 7954 1.196808 GCCAAGACACAACCATGTACG 59.803 52.381 0.00 0.00 37.82 3.67 R
7914 9952 0.399454 CATCCAAGATCTCCCGGCAT 59.601 55.000 0.00 0.00 0.00 4.40 R
8783 10858 1.000163 AGTTCACTCTGCAGGTGTACG 60.000 52.381 25.12 11.35 39.05 3.67 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
34 36 5.220265 GGCATGCATGTTAGAAAAATGTTCG 60.220 40.000 26.79 0.00 0.00 3.95
51 54 4.124238 TGTTCGGTAAAGTTGGTCTCAAG 58.876 43.478 0.00 0.00 32.92 3.02
290 619 4.523083 GGGGTTGACATATGCAGTAGAAA 58.477 43.478 1.58 0.00 0.00 2.52
456 811 0.697854 GGGCCTTGGATCCCCTTCTA 60.698 60.000 9.90 0.00 36.50 2.10
552 911 3.319198 GTGGGAGCGTGGGGAGAA 61.319 66.667 0.00 0.00 0.00 2.87
622 986 2.356553 TTCGGTGGTCGCTTTCCG 60.357 61.111 0.00 0.00 43.65 4.30
629 993 0.105224 TGGTCGCTTTCCGTTTCTGA 59.895 50.000 0.00 0.00 38.35 3.27
723 1093 0.029567 CCACTAGACGCGTCCATCTC 59.970 60.000 34.08 10.65 0.00 2.75
724 1094 0.733150 CACTAGACGCGTCCATCTCA 59.267 55.000 34.08 12.51 0.00 3.27
725 1095 1.132453 CACTAGACGCGTCCATCTCAA 59.868 52.381 34.08 11.14 0.00 3.02
726 1096 1.816835 ACTAGACGCGTCCATCTCAAA 59.183 47.619 34.08 9.80 0.00 2.69
727 1097 2.230508 ACTAGACGCGTCCATCTCAAAA 59.769 45.455 34.08 8.80 0.00 2.44
728 1098 2.163818 AGACGCGTCCATCTCAAAAA 57.836 45.000 34.08 0.00 0.00 1.94
729 1099 2.699954 AGACGCGTCCATCTCAAAAAT 58.300 42.857 34.08 9.55 0.00 1.82
730 1100 2.673368 AGACGCGTCCATCTCAAAAATC 59.327 45.455 34.08 6.15 0.00 2.17
731 1101 1.737793 ACGCGTCCATCTCAAAAATCC 59.262 47.619 5.58 0.00 0.00 3.01
732 1102 2.009774 CGCGTCCATCTCAAAAATCCT 58.990 47.619 0.00 0.00 0.00 3.24
733 1103 2.223112 CGCGTCCATCTCAAAAATCCTG 60.223 50.000 0.00 0.00 0.00 3.86
734 1104 2.749621 GCGTCCATCTCAAAAATCCTGT 59.250 45.455 0.00 0.00 0.00 4.00
735 1105 3.938963 GCGTCCATCTCAAAAATCCTGTA 59.061 43.478 0.00 0.00 0.00 2.74
736 1106 4.394920 GCGTCCATCTCAAAAATCCTGTAA 59.605 41.667 0.00 0.00 0.00 2.41
737 1107 5.106317 GCGTCCATCTCAAAAATCCTGTAAA 60.106 40.000 0.00 0.00 0.00 2.01
738 1108 6.314784 CGTCCATCTCAAAAATCCTGTAAAC 58.685 40.000 0.00 0.00 0.00 2.01
739 1109 6.149474 CGTCCATCTCAAAAATCCTGTAAACT 59.851 38.462 0.00 0.00 0.00 2.66
740 1110 7.308589 CGTCCATCTCAAAAATCCTGTAAACTT 60.309 37.037 0.00 0.00 0.00 2.66
741 1111 8.360390 GTCCATCTCAAAAATCCTGTAAACTTT 58.640 33.333 0.00 0.00 0.00 2.66
742 1112 9.581289 TCCATCTCAAAAATCCTGTAAACTTTA 57.419 29.630 0.00 0.00 0.00 1.85
743 1113 9.626045 CCATCTCAAAAATCCTGTAAACTTTAC 57.374 33.333 4.90 4.90 0.00 2.01
746 1116 9.621629 TCTCAAAAATCCTGTAAACTTTACAGA 57.378 29.630 30.91 21.15 45.69 3.41
747 1117 9.665264 CTCAAAAATCCTGTAAACTTTACAGAC 57.335 33.333 30.91 4.63 45.69 3.51
748 1118 9.403583 TCAAAAATCCTGTAAACTTTACAGACT 57.596 29.630 30.91 19.60 45.69 3.24
781 1151 9.601810 AGGGATAACTGTATTTTCTTCCTTTTT 57.398 29.630 0.00 0.00 0.00 1.94
808 1178 6.656270 AGGGTAACTGTAAATTTTAAGGACCG 59.344 38.462 0.00 0.00 0.00 4.79
864 1268 2.821685 CGATCCAATCGGAGCCCA 59.178 61.111 1.46 0.00 45.46 5.36
877 1281 2.665603 GCCCAAGGCTCTCTCGTT 59.334 61.111 0.00 0.00 46.69 3.85
878 1282 1.448717 GCCCAAGGCTCTCTCGTTC 60.449 63.158 0.00 0.00 46.69 3.95
879 1283 1.219393 CCCAAGGCTCTCTCGTTCC 59.781 63.158 0.00 0.00 0.00 3.62
880 1284 1.219393 CCAAGGCTCTCTCGTTCCC 59.781 63.158 0.00 0.00 0.00 3.97
881 1285 1.261238 CCAAGGCTCTCTCGTTCCCT 61.261 60.000 0.00 0.00 0.00 4.20
882 1286 0.610687 CAAGGCTCTCTCGTTCCCTT 59.389 55.000 0.00 0.00 36.38 3.95
883 1287 0.899019 AAGGCTCTCTCGTTCCCTTC 59.101 55.000 0.00 0.00 30.38 3.46
884 1288 1.139947 GGCTCTCTCGTTCCCTTCG 59.860 63.158 0.00 0.00 0.00 3.79
995 1405 4.982701 ACCCACCAAGCAGCAGGC 62.983 66.667 3.90 0.00 45.30 4.85
1102 1515 1.749033 CCCTTCCAGGTATCTCGCC 59.251 63.158 0.00 0.00 31.93 5.54
1108 1523 1.182385 CCAGGTATCTCGCCTCCCTC 61.182 65.000 0.00 0.00 33.31 4.30
1114 1529 2.956077 ATCTCGCCTCCCTCCCTTCC 62.956 65.000 0.00 0.00 0.00 3.46
1123 1538 3.330720 CTCCCTTCCCCCGCTGTT 61.331 66.667 0.00 0.00 0.00 3.16
1124 1539 3.628646 CTCCCTTCCCCCGCTGTTG 62.629 68.421 0.00 0.00 0.00 3.33
1163 1586 2.103143 CTCGACGAGCTTCGCCAT 59.897 61.111 12.67 0.00 45.12 4.40
1211 2201 1.227556 CCCTCCCCGAATTAGTGCG 60.228 63.158 0.00 0.00 0.00 5.34
1297 2287 3.798511 CTTTCCCCGGCCCTCTCC 61.799 72.222 0.00 0.00 0.00 3.71
1541 2544 4.828925 GTGCGGCTGAGAGGGCTC 62.829 72.222 0.00 0.00 41.67 4.70
1558 2561 0.615331 CTCTTGGCTGGGACTTAGCA 59.385 55.000 0.00 0.00 42.88 3.49
1585 2588 2.492088 TCGATTCGTCTGACCTCAACAT 59.508 45.455 5.89 0.00 0.00 2.71
1614 2617 4.464112 GAACCGCGCTATTTTGATAATCC 58.536 43.478 5.56 0.00 0.00 3.01
1755 2775 7.054491 TCAGCAACATTCAGCTATATAGTCA 57.946 36.000 11.38 0.00 39.50 3.41
1760 2780 7.763528 GCAACATTCAGCTATATAGTCAGCTAT 59.236 37.037 11.38 0.00 46.26 2.97
1787 2807 0.389037 TGACAGTTAGCGCTGCTGAG 60.389 55.000 34.63 19.29 40.10 3.35
1821 2846 2.634982 ATGTATTGCGTGCACCTTTG 57.365 45.000 12.15 0.00 0.00 2.77
1961 2986 5.039920 TGCTTGCTATGGTTACTGATGAT 57.960 39.130 0.00 0.00 0.00 2.45
2026 3051 2.514726 ATATCCCCTGGTTGCTACCT 57.485 50.000 18.31 0.00 45.27 3.08
2027 3052 1.802553 TATCCCCTGGTTGCTACCTC 58.197 55.000 18.31 0.00 45.27 3.85
2030 3055 1.923395 CCCTGGTTGCTACCTCCCA 60.923 63.158 18.31 0.00 45.27 4.37
2031 3056 1.299976 CCTGGTTGCTACCTCCCAC 59.700 63.158 18.31 0.00 45.27 4.61
2060 3086 3.820467 TGGTGCTCAAGAAAAACGATGAT 59.180 39.130 0.00 0.00 0.00 2.45
2173 3201 6.161855 AGAAGTACATGTCTTGTGTTGAGA 57.838 37.500 0.00 0.00 39.48 3.27
2270 3299 7.201600 GCTTTGGCAATTTGTGTTTAGAAGAAA 60.202 33.333 0.00 0.00 38.54 2.52
2274 3303 7.437862 TGGCAATTTGTGTTTAGAAGAAATGAC 59.562 33.333 0.00 0.00 0.00 3.06
2296 3325 2.265367 TCCCTGCTCCATGACAAACTA 58.735 47.619 0.00 0.00 0.00 2.24
2300 3329 2.744202 CTGCTCCATGACAAACTACACC 59.256 50.000 0.00 0.00 0.00 4.16
2311 3340 2.440539 AACTACACCAGCTGAGAACG 57.559 50.000 17.39 0.00 0.00 3.95
2370 3405 2.027385 CTTAGGGCCTCTTTGGAATGC 58.973 52.381 10.74 0.00 38.35 3.56
2371 3406 0.998928 TAGGGCCTCTTTGGAATGCA 59.001 50.000 10.74 0.00 38.35 3.96
2372 3407 0.337428 AGGGCCTCTTTGGAATGCAT 59.663 50.000 0.00 0.00 38.35 3.96
2373 3408 1.570501 AGGGCCTCTTTGGAATGCATA 59.429 47.619 0.00 0.00 38.35 3.14
2374 3409 2.178544 AGGGCCTCTTTGGAATGCATAT 59.821 45.455 0.00 0.00 38.35 1.78
2375 3410 2.298163 GGGCCTCTTTGGAATGCATATG 59.702 50.000 0.84 0.00 38.35 1.78
2421 3456 4.445448 GCCATGACTTCCTGGATCTTACAT 60.445 45.833 0.00 0.00 34.24 2.29
2574 3615 4.422073 TGTTGGAGAGCAACCCATATAG 57.578 45.455 0.00 0.00 31.66 1.31
2627 3668 9.101655 CCAAAGGGCTTCTATTCAAAAATAATG 57.898 33.333 0.00 0.00 0.00 1.90
2726 3768 1.611673 GGATAATGGATCACCTGGCGG 60.612 57.143 0.00 0.00 36.12 6.13
2747 3789 3.181523 GGTAGCCGAACTTCGAAAATGAC 60.182 47.826 12.87 2.33 43.74 3.06
3007 4053 5.300286 AGCAATGGGTAGAAACTATTGATGC 59.700 40.000 5.35 0.00 34.72 3.91
3052 4099 8.177663 ACTATCTTTTCATACTTCATGCAAACG 58.822 33.333 0.00 0.00 34.35 3.60
3101 4151 4.284378 GCTAATGGCACTGTTCTCATTC 57.716 45.455 0.00 0.00 41.35 2.67
3276 4327 6.151144 GGTTAGTTGATGCTAAAACCAGACAT 59.849 38.462 0.00 0.00 33.34 3.06
3375 4426 8.839343 TCATCGTAACTGAATTTGCAATATCAT 58.161 29.630 13.24 4.82 0.00 2.45
3376 4427 9.454585 CATCGTAACTGAATTTGCAATATCATT 57.545 29.630 13.24 4.72 0.00 2.57
3487 4538 4.717233 TTGACTCTTGTGCAATTTGTGT 57.283 36.364 0.00 0.00 0.00 3.72
4352 5406 7.354751 TGCCTACCTTTTGTCTTTGTAAATT 57.645 32.000 0.00 0.00 0.00 1.82
4431 5485 8.608185 ACATAAATAAGGTTCCAATCCATGTT 57.392 30.769 0.00 0.00 0.00 2.71
4763 5817 0.843309 TGCCTTCTGTCCTTGTTCCA 59.157 50.000 0.00 0.00 0.00 3.53
5216 6290 3.650461 TGCTTACTGCCCATGGTATGATA 59.350 43.478 11.73 0.00 42.00 2.15
5248 6322 6.855763 TTGAAGCCATAACCATCAAGAATT 57.144 33.333 0.00 0.00 0.00 2.17
5597 6671 6.062095 ACCAGAGCAACATATTATTGGTACC 58.938 40.000 4.43 4.43 37.88 3.34
5750 6930 3.933861 AGTTGACTCAAACCAGGAAGT 57.066 42.857 0.00 0.00 0.00 3.01
5790 6970 4.744795 ATACCACAGTCATGTCTTCCTC 57.255 45.455 0.00 0.00 37.65 3.71
6001 7182 3.554692 GCGAGATGGCGTTCACGG 61.555 66.667 0.81 0.00 40.23 4.94
6170 7352 7.209475 TCAAATTTTGTTGAGAATTGGGACTC 58.791 34.615 8.89 0.00 32.56 3.36
6208 7390 0.877743 GCTCCTTCCTGAACAAGTGC 59.122 55.000 0.00 0.00 0.00 4.40
6261 7443 6.560003 ATCCAGTTGTGGTTACTGATGATA 57.440 37.500 4.66 0.00 44.52 2.15
6280 7462 9.391006 TGATGATAATGTACCTTTGGTAGTTTC 57.609 33.333 0.00 0.00 39.02 2.78
6330 7512 5.912892 TGACTTTCCAGTTCCAAAATTTCC 58.087 37.500 0.00 0.00 31.22 3.13
6673 7856 8.133024 TGAAGATTTTTGGTACCTATTTGCAT 57.867 30.769 14.36 0.00 0.00 3.96
6771 7954 5.851703 GGAAGTTTTCGTAGATGCAGTTTTC 59.148 40.000 0.00 0.00 35.04 2.29
6991 9028 1.002468 ACTGCGAAACATGTTGAGCAC 60.002 47.619 27.09 11.86 34.06 4.40
7228 9266 3.766591 TGTTCCTTCCTTTTGTGAAGCAA 59.233 39.130 0.00 0.00 38.29 3.91
7789 9827 8.134202 TGATCTGTCTCTTTACAAGGTATTCA 57.866 34.615 0.00 0.00 0.00 2.57
7798 9836 8.827177 TCTTTACAAGGTATTCACTGTTACAG 57.173 34.615 11.21 11.21 37.52 2.74
8293 10332 5.291128 ACAGATTATGGAAAAGTTCGTAGCG 59.709 40.000 0.00 0.00 0.00 4.26
8422 10461 0.035881 CTCAAGAGGAGTGGCTTGCA 59.964 55.000 0.00 0.00 40.89 4.08
8492 10531 4.367450 GAAGACGAGGATGAAGATGAAGG 58.633 47.826 0.00 0.00 0.00 3.46
8522 10561 2.038426 TGGAGTGACCATGGTACAACAG 59.962 50.000 19.80 0.00 44.64 3.16
8565 10604 6.500684 TGTAGCAGAAAAGATTGTGGAATC 57.499 37.500 0.00 0.00 38.69 2.52
8595 10634 1.001048 TGTGCTGAAAACAGAGCATGC 60.001 47.619 10.51 10.51 46.51 4.06
8718 10776 7.748691 TGATTTCTGAAGATGTGTTTGATCA 57.251 32.000 0.00 0.00 0.00 2.92
8720 10778 5.596268 TTCTGAAGATGTGTTTGATCACG 57.404 39.130 0.00 0.00 40.74 4.35
8744 10819 1.238439 TGCTGCAGCTAAAAGGTGTC 58.762 50.000 36.61 6.43 44.96 3.67
8783 10858 2.095718 GTCTGAAACTCACATTTCGGGC 60.096 50.000 7.11 2.20 42.76 6.13
8789 10864 0.719465 CTCACATTTCGGGCGTACAC 59.281 55.000 0.00 0.00 0.00 2.90
8811 10886 1.272490 TGCAGAGTGAACTTAGGACGG 59.728 52.381 0.00 0.00 0.00 4.79
8857 10932 4.706842 ACAGAAATGTTGTACTCCCTGT 57.293 40.909 0.00 0.00 0.00 4.00
8876 10953 6.100134 TCCCTGTAACTTTGTACTAAACCAGT 59.900 38.462 0.00 0.00 41.62 4.00
8890 10967 9.865321 GTACTAAACCAGTGACAAGTAATATGA 57.135 33.333 0.00 0.00 38.24 2.15
8977 11371 4.793216 GCATGGTTGAGCTTTTATGTAACG 59.207 41.667 0.00 0.00 0.00 3.18
8987 11382 2.018542 TTATGTAACGCCAGGACAGC 57.981 50.000 0.00 0.00 0.00 4.40
9093 11751 3.924686 ACTTAGAACAAAGCGGACATACG 59.075 43.478 0.00 0.00 0.00 3.06
9122 11780 1.337728 TGAGATCGCGTTTGACATGGT 60.338 47.619 5.77 0.00 0.00 3.55
9164 11824 2.290641 GCCTGGTTTAGCCACGATAATG 59.709 50.000 0.00 0.00 43.61 1.90
9177 11837 5.118990 CCACGATAATGATCTTTGTGTCCT 58.881 41.667 4.17 0.00 0.00 3.85
9178 11838 6.280643 CCACGATAATGATCTTTGTGTCCTA 58.719 40.000 4.17 0.00 0.00 2.94
9180 11840 6.201044 CACGATAATGATCTTTGTGTCCTACC 59.799 42.308 4.17 0.00 0.00 3.18
9181 11841 6.098409 ACGATAATGATCTTTGTGTCCTACCT 59.902 38.462 4.17 0.00 0.00 3.08
9182 11842 7.287005 ACGATAATGATCTTTGTGTCCTACCTA 59.713 37.037 4.17 0.00 0.00 3.08
9183 11843 8.141909 CGATAATGATCTTTGTGTCCTACCTAA 58.858 37.037 4.17 0.00 0.00 2.69
9184 11844 9.832445 GATAATGATCTTTGTGTCCTACCTAAA 57.168 33.333 4.17 0.00 0.00 1.85
9185 11845 7.923414 AATGATCTTTGTGTCCTACCTAAAC 57.077 36.000 0.00 0.00 0.00 2.01
9186 11846 5.801380 TGATCTTTGTGTCCTACCTAAACC 58.199 41.667 0.00 0.00 0.00 3.27
9187 11847 4.628963 TCTTTGTGTCCTACCTAAACCC 57.371 45.455 0.00 0.00 0.00 4.11
9188 11848 3.328637 TCTTTGTGTCCTACCTAAACCCC 59.671 47.826 0.00 0.00 0.00 4.95
9189 11849 2.727429 TGTGTCCTACCTAAACCCCT 57.273 50.000 0.00 0.00 0.00 4.79
9190 11850 2.262637 TGTGTCCTACCTAAACCCCTG 58.737 52.381 0.00 0.00 0.00 4.45
9191 11851 2.263545 GTGTCCTACCTAAACCCCTGT 58.736 52.381 0.00 0.00 0.00 4.00
9194 11854 3.073356 TGTCCTACCTAAACCCCTGTTTG 59.927 47.826 1.14 0.00 44.27 2.93
9203 11863 3.726517 CCCTGTTTGGCGACGCAG 61.727 66.667 23.09 9.68 0.00 5.18
9221 11881 1.129998 CAGCCAACTCGAATTGCTCTG 59.870 52.381 0.00 6.87 0.00 3.35
9226 11886 1.222936 CTCGAATTGCTCTGGGCCT 59.777 57.895 4.53 0.00 40.92 5.19
9240 11900 3.772572 TCTGGGCCTATTATAATAGCGCA 59.227 43.478 28.29 27.22 37.61 6.09
9309 11970 2.439701 TCGCCGAGTTCCGATCCT 60.440 61.111 0.00 0.00 41.76 3.24
9332 11997 1.202154 CGTACATCTCGAGAAAGGCGT 60.202 52.381 20.91 13.50 0.00 5.68
9333 11998 2.031314 CGTACATCTCGAGAAAGGCGTA 59.969 50.000 20.91 12.55 0.00 4.42
9334 11999 2.563471 ACATCTCGAGAAAGGCGTAC 57.437 50.000 20.91 0.00 0.00 3.67
9335 12000 1.202154 ACATCTCGAGAAAGGCGTACG 60.202 52.381 20.91 11.84 0.00 3.67
9336 12001 1.093159 ATCTCGAGAAAGGCGTACGT 58.907 50.000 20.91 0.00 0.00 3.57
9338 12003 0.856490 CTCGAGAAAGGCGTACGTCG 60.856 60.000 17.90 16.29 43.12 5.12
9339 12004 1.133253 CGAGAAAGGCGTACGTCGA 59.867 57.895 17.90 0.00 42.86 4.20
9355 12020 4.077184 GACGGGCCATCGGTGACA 62.077 66.667 4.39 0.00 0.00 3.58
9443 12108 2.956964 CTAGAGAAAGGCGCCGCG 60.957 66.667 23.20 8.83 0.00 6.46
9471 12136 3.061848 CGGCGACAAGGGGCAAAT 61.062 61.111 0.00 0.00 0.00 2.32
9472 12137 2.635443 CGGCGACAAGGGGCAAATT 61.635 57.895 0.00 0.00 0.00 1.82
9473 12138 1.671166 GGCGACAAGGGGCAAATTT 59.329 52.632 0.00 0.00 0.00 1.82
9474 12139 0.670239 GGCGACAAGGGGCAAATTTG 60.670 55.000 14.03 14.03 0.00 2.32
9475 12140 0.316841 GCGACAAGGGGCAAATTTGA 59.683 50.000 22.31 0.00 0.00 2.69
9476 12141 1.934849 GCGACAAGGGGCAAATTTGAC 60.935 52.381 22.31 19.34 34.70 3.18
9477 12142 1.339610 CGACAAGGGGCAAATTTGACA 59.660 47.619 25.05 0.00 38.18 3.58
9478 12143 2.223923 CGACAAGGGGCAAATTTGACAA 60.224 45.455 25.05 0.00 38.18 3.18
9479 12144 3.739519 CGACAAGGGGCAAATTTGACAAA 60.740 43.478 25.05 2.48 38.18 2.83
9480 12145 4.388485 GACAAGGGGCAAATTTGACAAAT 58.612 39.130 25.05 7.62 38.18 2.32
9481 12146 4.790937 ACAAGGGGCAAATTTGACAAATT 58.209 34.783 25.05 18.41 42.62 1.82
9483 12148 6.360618 ACAAGGGGCAAATTTGACAAATTTA 58.639 32.000 29.34 0.00 46.34 1.40
9484 12149 6.830838 ACAAGGGGCAAATTTGACAAATTTAA 59.169 30.769 29.34 0.00 46.34 1.52
9485 12150 6.875948 AGGGGCAAATTTGACAAATTTAAC 57.124 33.333 29.34 24.33 46.34 2.01
9486 12151 5.767665 AGGGGCAAATTTGACAAATTTAACC 59.232 36.000 29.34 29.17 46.34 2.85
9487 12152 5.767665 GGGGCAAATTTGACAAATTTAACCT 59.232 36.000 31.84 17.15 46.34 3.50
9488 12153 6.937465 GGGGCAAATTTGACAAATTTAACCTA 59.063 34.615 31.84 5.58 46.34 3.08
9489 12154 7.609918 GGGGCAAATTTGACAAATTTAACCTAT 59.390 33.333 31.84 16.16 46.34 2.57
9490 12155 9.660180 GGGCAAATTTGACAAATTTAACCTATA 57.340 29.630 31.84 4.60 46.34 1.31
9506 12171 8.984891 TTAACCTATAGACGAAAACAAATCGA 57.015 30.769 0.00 0.00 42.76 3.59
9507 12172 7.894376 AACCTATAGACGAAAACAAATCGAA 57.106 32.000 0.00 0.00 42.76 3.71
9508 12173 7.287050 ACCTATAGACGAAAACAAATCGAAC 57.713 36.000 0.00 0.00 42.76 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 2.858745 TGGCTTGAGACCAACTTTACC 58.141 47.619 0.00 0.00 33.12 2.85
51 54 5.120053 GGTTTAGTTGCACAATAAACATGGC 59.880 40.000 21.74 9.81 39.86 4.40
456 811 1.902508 TGCCTTCTTCTTCTCCACGAT 59.097 47.619 0.00 0.00 0.00 3.73
512 869 2.317040 GGCCAGCTATACCTACACAGA 58.683 52.381 0.00 0.00 0.00 3.41
516 873 1.037493 CGTGGCCAGCTATACCTACA 58.963 55.000 5.11 0.00 0.00 2.74
552 911 3.829026 GCCCAAACAGAAGGAGAGAAAAT 59.171 43.478 0.00 0.00 0.00 1.82
622 986 2.677979 GGTCCCGCGCTTCAGAAAC 61.678 63.158 5.56 0.00 0.00 2.78
651 1020 2.617276 GCCGGCCTAAAAAGGTAAGTCT 60.617 50.000 18.11 0.00 0.00 3.24
755 1125 9.601810 AAAAAGGAAGAAAATACAGTTATCCCT 57.398 29.630 0.00 0.00 0.00 4.20
781 1151 9.519191 GGTCCTTAAAATTTACAGTTACCCTTA 57.481 33.333 0.00 0.00 0.00 2.69
782 1152 7.175467 CGGTCCTTAAAATTTACAGTTACCCTT 59.825 37.037 0.00 0.00 0.00 3.95
783 1153 6.656270 CGGTCCTTAAAATTTACAGTTACCCT 59.344 38.462 0.00 0.00 0.00 4.34
784 1154 6.654582 TCGGTCCTTAAAATTTACAGTTACCC 59.345 38.462 0.00 0.00 0.00 3.69
785 1155 7.671495 TCGGTCCTTAAAATTTACAGTTACC 57.329 36.000 0.00 0.70 0.00 2.85
786 1156 9.385902 GTTTCGGTCCTTAAAATTTACAGTTAC 57.614 33.333 0.00 0.00 0.00 2.50
787 1157 8.281893 CGTTTCGGTCCTTAAAATTTACAGTTA 58.718 33.333 0.00 0.00 0.00 2.24
788 1158 7.012232 TCGTTTCGGTCCTTAAAATTTACAGTT 59.988 33.333 0.00 0.00 0.00 3.16
789 1159 6.482973 TCGTTTCGGTCCTTAAAATTTACAGT 59.517 34.615 0.00 0.00 0.00 3.55
797 1167 3.191078 TGGTCGTTTCGGTCCTTAAAA 57.809 42.857 0.00 0.00 0.00 1.52
802 1172 1.301479 GCTTGGTCGTTTCGGTCCT 60.301 57.895 0.00 0.00 0.00 3.85
808 1178 0.789383 CGCGATTGCTTGGTCGTTTC 60.789 55.000 0.00 0.00 39.87 2.78
861 1265 1.219393 GGAACGAGAGAGCCTTGGG 59.781 63.158 0.00 0.00 0.00 4.12
864 1268 0.899019 GAAGGGAACGAGAGAGCCTT 59.101 55.000 0.00 0.00 0.00 4.35
869 1273 1.451067 GAGACGAAGGGAACGAGAGA 58.549 55.000 0.00 0.00 34.70 3.10
870 1274 0.097325 CGAGACGAAGGGAACGAGAG 59.903 60.000 0.00 0.00 34.70 3.20
871 1275 1.919956 GCGAGACGAAGGGAACGAGA 61.920 60.000 0.00 0.00 34.70 4.04
872 1276 1.514443 GCGAGACGAAGGGAACGAG 60.514 63.158 0.00 0.00 34.70 4.18
873 1277 1.919956 GAGCGAGACGAAGGGAACGA 61.920 60.000 0.00 0.00 34.70 3.85
874 1278 1.514443 GAGCGAGACGAAGGGAACG 60.514 63.158 0.00 0.00 0.00 3.95
875 1279 1.153804 GGAGCGAGACGAAGGGAAC 60.154 63.158 0.00 0.00 0.00 3.62
876 1280 2.348888 GGGAGCGAGACGAAGGGAA 61.349 63.158 0.00 0.00 0.00 3.97
877 1281 2.754658 GGGAGCGAGACGAAGGGA 60.755 66.667 0.00 0.00 0.00 4.20
878 1282 2.756283 AGGGAGCGAGACGAAGGG 60.756 66.667 0.00 0.00 0.00 3.95
879 1283 1.316706 AAGAGGGAGCGAGACGAAGG 61.317 60.000 0.00 0.00 0.00 3.46
880 1284 0.528470 AAAGAGGGAGCGAGACGAAG 59.472 55.000 0.00 0.00 0.00 3.79
881 1285 0.526662 GAAAGAGGGAGCGAGACGAA 59.473 55.000 0.00 0.00 0.00 3.85
882 1286 0.322636 AGAAAGAGGGAGCGAGACGA 60.323 55.000 0.00 0.00 0.00 4.20
883 1287 0.528470 AAGAAAGAGGGAGCGAGACG 59.472 55.000 0.00 0.00 0.00 4.18
884 1288 2.612604 GAAAGAAAGAGGGAGCGAGAC 58.387 52.381 0.00 0.00 0.00 3.36
923 1327 1.380650 GGCGGGAAGAGAGAGAGGT 60.381 63.158 0.00 0.00 0.00 3.85
924 1328 1.076339 AGGCGGGAAGAGAGAGAGG 60.076 63.158 0.00 0.00 0.00 3.69
925 1329 0.682855 ACAGGCGGGAAGAGAGAGAG 60.683 60.000 0.00 0.00 0.00 3.20
931 1335 4.821589 GCGGACAGGCGGGAAGAG 62.822 72.222 0.00 0.00 0.00 2.85
973 1383 2.133641 GCTGCTTGGTGGGTGGTTT 61.134 57.895 0.00 0.00 0.00 3.27
974 1384 2.521708 GCTGCTTGGTGGGTGGTT 60.522 61.111 0.00 0.00 0.00 3.67
1108 1523 4.740822 CCAACAGCGGGGGAAGGG 62.741 72.222 0.00 0.00 0.00 3.95
1114 1529 4.038080 GCGTTTCCAACAGCGGGG 62.038 66.667 0.00 0.00 0.00 5.73
1141 1556 4.778415 GAAGCTCGTCGAGGCGCA 62.778 66.667 23.09 0.00 0.00 6.09
1159 1582 2.101770 GCTTCAGCGCAGAATGGC 59.898 61.111 16.00 12.80 35.86 4.40
1289 2279 4.467107 ACGAGGAGGGGAGAGGGC 62.467 72.222 0.00 0.00 0.00 5.19
1408 2411 2.035626 CAGCCCAAATCCACCCGT 59.964 61.111 0.00 0.00 0.00 5.28
1451 2454 2.909965 AAACGGTTGGCATGCGGT 60.910 55.556 12.44 1.35 0.00 5.68
1541 2544 0.326264 ACTGCTAAGTCCCAGCCAAG 59.674 55.000 0.00 0.00 38.29 3.61
1558 2561 1.405821 GGTCAGACGAATCGATCCACT 59.594 52.381 10.55 0.00 0.00 4.00
1585 2588 0.464036 AATAGCGCGGTTCCTGATCA 59.536 50.000 19.09 0.00 0.00 2.92
1614 2617 0.719465 GTATGGTGTTTGTCGCTCCG 59.281 55.000 0.00 0.00 0.00 4.63
1755 2775 6.183360 GCGCTAACTGTCAGATCTATATAGCT 60.183 42.308 6.91 0.00 33.01 3.32
1758 2778 6.403746 GCAGCGCTAACTGTCAGATCTATATA 60.404 42.308 10.99 0.00 39.96 0.86
1760 2780 4.320567 GCAGCGCTAACTGTCAGATCTATA 60.321 45.833 10.99 0.00 39.96 1.31
1762 2782 2.223595 GCAGCGCTAACTGTCAGATCTA 60.224 50.000 10.99 0.00 39.96 1.98
1768 2788 0.389037 CTCAGCAGCGCTAACTGTCA 60.389 55.000 28.72 16.13 36.40 3.58
1787 2807 9.158364 CACGCAATACATAAAGATGTCAAATAC 57.842 33.333 0.00 0.00 43.01 1.89
2129 3156 5.547465 TCTTTGAACATACCGAACATGAGT 58.453 37.500 0.00 0.00 0.00 3.41
2173 3201 7.394359 ACTTATTGTTGAATAGACAAGGTGCAT 59.606 33.333 0.00 0.00 40.04 3.96
2270 3299 1.142465 GTCATGGAGCAGGGATGTCAT 59.858 52.381 0.00 0.00 0.00 3.06
2274 3303 1.747355 GTTTGTCATGGAGCAGGGATG 59.253 52.381 0.00 0.00 0.00 3.51
2296 3325 3.142393 AGCGTTCTCAGCTGGTGT 58.858 55.556 15.13 0.00 44.22 4.16
2311 3340 2.119457 CTGCAAAAGAAAACGGACAGC 58.881 47.619 0.00 0.00 0.00 4.40
2328 3357 3.988517 GGGTGCGAGTATAATAAGACTGC 59.011 47.826 0.00 0.00 0.00 4.40
2344 3379 2.198304 AAAGAGGCCCTAAGGGTGCG 62.198 60.000 0.00 0.00 46.51 5.34
2421 3456 5.581126 AAAGAGACATGTTTGCAAGTTCA 57.419 34.783 0.00 1.34 0.00 3.18
2503 3540 9.642343 GGGGTTAGACCTTATGAAAATTATTCT 57.358 33.333 0.00 0.00 38.64 2.40
2532 3569 8.197439 CCAACATCCCAATTTTAAAGGATCTAC 58.803 37.037 4.20 0.00 36.99 2.59
2667 3709 0.682209 CCAGCTCTTCCCATGGGTTG 60.682 60.000 30.28 22.32 36.47 3.77
2726 3768 3.181523 GGTCATTTTCGAAGTTCGGCTAC 60.182 47.826 24.18 13.46 40.88 3.58
2747 3789 5.869649 TTTGAGGAAGGAAAAGAAAAGGG 57.130 39.130 0.00 0.00 0.00 3.95
3052 4099 2.191128 AGGAACCATGCAGAGTTCAC 57.809 50.000 24.83 17.05 43.37 3.18
3101 4151 5.712152 AAGTCAAAAGTTATGAAGGCCAG 57.288 39.130 5.01 0.00 0.00 4.85
3140 4190 1.997311 TGCCCCCAGTGATCTCCTG 60.997 63.158 0.00 6.12 0.00 3.86
3276 4327 6.912051 GCAATTCGAAATGTGCTGTATCAATA 59.088 34.615 19.06 0.00 34.13 1.90
3638 4691 5.378230 TCTTCTGCCCAATTCAGACATAT 57.622 39.130 0.00 0.00 39.99 1.78
4322 5376 3.898482 AGACAAAAGGTAGGCAACAGTT 58.102 40.909 0.00 0.00 41.41 3.16
4431 5485 5.940470 GCTAGTTCTTTTTCCAGAGGATTGA 59.060 40.000 0.00 0.00 0.00 2.57
4763 5817 5.449553 AGACCACAAGAAGAAGATGGTTTT 58.550 37.500 0.00 0.00 43.73 2.43
4877 5932 7.855904 CACTTGGCCAAATAATTAGTTACGATC 59.144 37.037 20.91 0.00 0.00 3.69
5216 6290 4.898861 TGGTTATGGCTTCAAAAGAAACCT 59.101 37.500 0.00 0.00 36.83 3.50
5248 6322 9.723601 ACCAACGTAGAAAAATAAAGGTATGTA 57.276 29.630 0.00 0.00 0.00 2.29
5289 6363 5.013599 GGAGCTAGATTCCATCCCTGTAAAT 59.986 44.000 8.43 0.00 34.74 1.40
5597 6671 8.137437 AGAAGTGAACCAAAAATACAGACAATG 58.863 33.333 0.00 0.00 0.00 2.82
5846 7027 6.070194 AGGTATAACACATGTTTAGTCTGGCT 60.070 38.462 1.98 0.00 39.31 4.75
6001 7182 6.817765 TCATCTAACCCAATGTTCTGAAAC 57.182 37.500 0.00 0.00 38.42 2.78
6170 7352 4.034510 GGAGCCTCATTTTAAGATGACACG 59.965 45.833 4.62 0.00 32.82 4.49
6232 7414 2.897271 AACCACAACTGGATATGCCA 57.103 45.000 0.00 0.00 46.96 4.92
6233 7415 3.627577 CAGTAACCACAACTGGATATGCC 59.372 47.826 0.00 0.00 40.55 4.40
6246 7428 8.612619 CAAAGGTACATTATCATCAGTAACCAC 58.387 37.037 0.00 0.00 0.00 4.16
6261 7443 7.231467 ACATGAGAAACTACCAAAGGTACATT 58.769 34.615 0.00 0.00 37.09 2.71
6330 7512 2.033801 CACACTTCAAAACCCAGCTGAG 59.966 50.000 17.39 3.79 0.00 3.35
6771 7954 1.196808 GCCAAGACACAACCATGTACG 59.803 52.381 0.00 0.00 37.82 3.67
6991 9028 8.319146 TCTGTAAATCCTCCAAAAACTACTAGG 58.681 37.037 0.00 0.00 0.00 3.02
7789 9827 7.394816 AGTATTGCCTCAATAACTGTAACAGT 58.605 34.615 0.00 0.00 39.48 3.55
7906 9944 2.239654 AGATCTCCCGGCATTTTCAGAA 59.760 45.455 0.00 0.00 0.00 3.02
7914 9952 0.399454 CATCCAAGATCTCCCGGCAT 59.601 55.000 0.00 0.00 0.00 4.40
7970 10008 3.507162 TGCAGGGAATGTTCTTGAGAA 57.493 42.857 0.00 0.00 0.00 2.87
8293 10332 2.234168 GAGTAGACAAAGGGTGAGGGAC 59.766 54.545 0.00 0.00 0.00 4.46
8422 10461 1.365633 GCCTCCGCGATGAGAAGAT 59.634 57.895 8.23 0.00 34.11 2.40
8595 10634 3.181526 GCTCATTGTGACTCAAAGCTACG 60.182 47.826 6.66 0.00 39.62 3.51
8602 10641 2.880268 CAGGTTGCTCATTGTGACTCAA 59.120 45.455 0.00 0.00 40.53 3.02
8685 10743 8.512956 ACACATCTTCAGAAATCAAAATCAGAG 58.487 33.333 0.00 0.00 0.00 3.35
8783 10858 1.000163 AGTTCACTCTGCAGGTGTACG 60.000 52.381 25.12 11.35 39.05 3.67
8789 10864 2.672478 CGTCCTAAGTTCACTCTGCAGG 60.672 54.545 15.13 7.28 0.00 4.85
8811 10886 4.083484 GCAACACCACCATTTACAGAGTAC 60.083 45.833 0.00 0.00 0.00 2.73
8857 10932 8.042515 ACTTGTCACTGGTTTAGTACAAAGTTA 58.957 33.333 0.00 0.00 37.60 2.24
8876 10953 5.600898 TCCCTCCGATTCATATTACTTGTCA 59.399 40.000 0.00 0.00 0.00 3.58
8890 10967 3.684408 AACTAGGTACTCCCTCCGATT 57.316 47.619 0.00 0.00 44.81 3.34
8953 11072 5.391950 CGTTACATAAAAGCTCAACCATGCT 60.392 40.000 0.00 0.00 41.82 3.79
8977 11371 2.331132 GCTTCAGTGCTGTCCTGGC 61.331 63.158 0.00 0.00 0.00 4.85
8987 11382 2.414481 CCAAGATGACTTCGCTTCAGTG 59.586 50.000 0.00 0.00 33.70 3.66
9048 11443 8.547967 AGTACGCTTTTGAGATGATTCTAAAA 57.452 30.769 0.00 0.00 31.52 1.52
9093 11751 1.373497 CGCGATCTCATGGGCTACC 60.373 63.158 0.00 0.00 37.24 3.18
9122 11780 1.228429 CCTTGTTTTGGGCCGAGGA 60.228 57.895 0.00 0.00 34.61 3.71
9164 11824 5.183969 GGGTTTAGGTAGGACACAAAGATC 58.816 45.833 0.00 0.00 0.00 2.75
9177 11837 1.271488 CGCCAAACAGGGGTTTAGGTA 60.271 52.381 0.00 0.00 45.18 3.08
9178 11838 0.538746 CGCCAAACAGGGGTTTAGGT 60.539 55.000 0.00 0.00 45.18 3.08
9186 11846 3.726517 CTGCGTCGCCAAACAGGG 61.727 66.667 15.88 0.00 38.09 4.45
9187 11847 4.389576 GCTGCGTCGCCAAACAGG 62.390 66.667 15.88 0.00 41.84 4.00
9203 11863 0.449388 CCAGAGCAATTCGAGTTGGC 59.551 55.000 20.52 13.18 0.00 4.52
9221 11881 4.065789 GGATGCGCTATTATAATAGGCCC 58.934 47.826 26.50 20.58 39.00 5.80
9226 11886 5.588240 CGGACAGGATGCGCTATTATAATA 58.412 41.667 9.73 5.10 42.53 0.98
9240 11900 0.391263 GGAAAGCGAACGGACAGGAT 60.391 55.000 0.00 0.00 0.00 3.24
9264 11925 2.285743 GGTGAGGGAGAGGGGCTT 60.286 66.667 0.00 0.00 0.00 4.35
9309 11970 2.022195 CCTTTCTCGAGATGTACGGGA 58.978 52.381 17.44 0.00 38.50 5.14
9332 11997 3.879682 CGATGGCCCGTCGACGTA 61.880 66.667 33.49 18.43 44.49 3.57
9338 12003 3.599285 TTGTCACCGATGGCCCGTC 62.599 63.158 0.00 0.00 0.00 4.79
9339 12004 3.632080 TTGTCACCGATGGCCCGT 61.632 61.111 0.00 0.00 0.00 5.28
9340 12005 3.124921 GTTGTCACCGATGGCCCG 61.125 66.667 0.00 0.00 0.00 6.13
9341 12006 3.124921 CGTTGTCACCGATGGCCC 61.125 66.667 0.00 0.00 0.00 5.80
9355 12020 2.356135 CTGACGGGGAATTGATTCGTT 58.644 47.619 0.00 0.00 37.67 3.85
9480 12145 9.421806 TCGATTTGTTTTCGTCTATAGGTTAAA 57.578 29.630 0.00 0.00 37.82 1.52
9481 12146 8.984891 TCGATTTGTTTTCGTCTATAGGTTAA 57.015 30.769 0.00 0.00 37.82 2.01
9482 12147 8.863049 GTTCGATTTGTTTTCGTCTATAGGTTA 58.137 33.333 0.00 0.00 37.82 2.85
9483 12148 7.736447 GTTCGATTTGTTTTCGTCTATAGGTT 58.264 34.615 0.00 0.00 37.82 3.50
9484 12149 7.287050 GTTCGATTTGTTTTCGTCTATAGGT 57.713 36.000 0.00 0.00 37.82 3.08


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

AutoCloner maintained by Alex Coulton.