Multiple sequence alignment - TraesCS5A01G214400

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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 TraesCS5A01G214400 chr5A 100.000 6350 0 0 1 6350 429980067 429986416 0.000000e+00 11727.0
1 TraesCS5A01G214400 chr5A 96.369 661 23 1 1 661 583623859 583623200 0.000000e+00 1086.0
2 TraesCS5A01G214400 chr5A 92.638 163 10 2 4445 4605 320214244 320214406 3.830000e-57 233.0
3 TraesCS5A01G214400 chr5D 95.621 5252 140 37 692 5899 326461428 326456223 0.000000e+00 8342.0
4 TraesCS5A01G214400 chr5B 94.918 3778 119 36 704 4446 379002477 378998738 0.000000e+00 5845.0
5 TraesCS5A01G214400 chr5B 91.374 1623 77 26 4603 6201 378998739 378997156 0.000000e+00 2163.0
6 TraesCS5A01G214400 chr5B 80.514 662 126 2 1 661 314976538 314977197 7.350000e-139 505.0
7 TraesCS5A01G214400 chr5B 92.121 165 11 2 4446 4608 407219553 407219389 1.380000e-56 231.0
8 TraesCS5A01G214400 chr5B 91.837 98 8 0 4213 4310 166379086 166379183 3.090000e-28 137.0
9 TraesCS5A01G214400 chr5B 97.222 36 0 1 5819 5853 474058538 474058503 6.880000e-05 60.2
10 TraesCS5A01G214400 chr6D 86.864 2124 189 42 2145 4219 411193395 411191313 0.000000e+00 2294.0
11 TraesCS5A01G214400 chr6D 79.471 794 95 38 1255 2034 411194286 411193547 9.500000e-138 501.0
12 TraesCS5A01G214400 chr6D 87.054 448 43 8 4564 5008 411191185 411190750 5.720000e-135 492.0
13 TraesCS5A01G214400 chr6D 85.145 276 35 6 5111 5383 411190459 411190187 1.740000e-70 278.0
14 TraesCS5A01G214400 chr6A 87.930 1135 103 19 2188 3295 555934072 555932945 0.000000e+00 1306.0
15 TraesCS5A01G214400 chr6A 90.275 946 77 11 3279 4214 555932934 555931994 0.000000e+00 1223.0
16 TraesCS5A01G214400 chr6A 97.277 661 17 1 1 661 120117208 120116549 0.000000e+00 1120.0
17 TraesCS5A01G214400 chr6A 79.068 1051 138 44 1001 2028 555935083 555934092 0.000000e+00 647.0
18 TraesCS5A01G214400 chr6A 90.365 384 28 4 4627 5008 555931974 555931598 4.420000e-136 496.0
19 TraesCS5A01G214400 chr6A 84.229 279 37 7 5111 5386 555931300 555931026 1.360000e-66 265.0
20 TraesCS5A01G214400 chr6A 82.143 140 12 3 5384 5510 555930998 555930859 2.420000e-19 108.0
21 TraesCS5A01G214400 chr6B 86.723 1175 114 25 2143 3295 617982994 617981840 0.000000e+00 1267.0
22 TraesCS5A01G214400 chr6B 90.496 947 74 13 3277 4214 617981828 617980889 0.000000e+00 1236.0
23 TraesCS5A01G214400 chr6B 79.611 1079 116 49 1001 2034 617984179 617983160 0.000000e+00 678.0
24 TraesCS5A01G214400 chr6B 88.803 518 31 11 4603 5109 617980753 617980252 1.510000e-170 610.0
25 TraesCS5A01G214400 chr6B 78.963 656 129 8 1 656 546088871 546089517 7.560000e-119 438.0
26 TraesCS5A01G214400 chr6B 77.810 694 69 40 5112 5723 617980035 617979345 3.640000e-92 350.0
27 TraesCS5A01G214400 chr6B 91.515 165 12 2 4443 4605 481857849 481858013 6.410000e-55 226.0
28 TraesCS5A01G214400 chr2A 95.921 662 24 2 2 661 478903988 478903328 0.000000e+00 1070.0
29 TraesCS5A01G214400 chr2A 92.073 164 11 2 4443 4604 419206979 419206816 4.950000e-56 230.0
30 TraesCS5A01G214400 chr2D 95.461 661 28 1 1 661 190432226 190432884 0.000000e+00 1053.0
31 TraesCS5A01G214400 chr2D 95.166 662 29 3 1 661 650975431 650976090 0.000000e+00 1042.0
32 TraesCS5A01G214400 chr2D 85.329 668 95 3 1 668 241695195 241694531 0.000000e+00 688.0
33 TraesCS5A01G214400 chr2D 91.753 97 8 0 4213 4309 74149732 74149828 1.110000e-27 135.0
34 TraesCS5A01G214400 chr3A 94.554 661 33 3 1 661 632541780 632541123 0.000000e+00 1018.0
35 TraesCS5A01G214400 chr3A 90.385 104 10 0 4213 4316 470095682 470095785 3.090000e-28 137.0
36 TraesCS5A01G214400 chr1B 92.716 659 43 4 1 658 527623611 527624265 0.000000e+00 946.0
37 TraesCS5A01G214400 chr1B 90.854 656 53 4 1 656 293589455 293588807 0.000000e+00 872.0
38 TraesCS5A01G214400 chr1B 92.025 163 11 2 4445 4605 666933539 666933701 1.780000e-55 228.0
39 TraesCS5A01G214400 chr7D 90.744 659 50 4 1 659 492774899 492775546 0.000000e+00 869.0
40 TraesCS5A01G214400 chr7D 91.000 100 9 0 4213 4312 580850179 580850080 1.110000e-27 135.0
41 TraesCS5A01G214400 chr2B 88.923 659 67 4 1 656 658203513 658204168 0.000000e+00 808.0
42 TraesCS5A01G214400 chr7A 93.910 509 30 1 153 661 427541448 427541955 0.000000e+00 767.0
43 TraesCS5A01G214400 chr3D 85.628 661 88 5 1 661 560262431 560261778 0.000000e+00 688.0
44 TraesCS5A01G214400 chr3D 92.073 164 11 2 4443 4604 375693992 375693829 4.950000e-56 230.0
45 TraesCS5A01G214400 chr3D 82.292 192 33 1 465 656 11475031 11474841 1.420000e-36 165.0
46 TraesCS5A01G214400 chr7B 84.488 664 95 6 1 661 183577751 183577093 0.000000e+00 649.0
47 TraesCS5A01G214400 chr7B 86.126 555 75 1 1 555 609889815 609889263 1.180000e-166 597.0
48 TraesCS5A01G214400 chr7B 88.430 121 12 2 4213 4331 162120908 162120788 1.850000e-30 145.0
49 TraesCS5A01G214400 chr4D 91.228 171 13 2 4436 4604 64390641 64390471 1.380000e-56 231.0
50 TraesCS5A01G214400 chr3B 93.038 158 10 1 4445 4601 529407790 529407947 4.950000e-56 230.0
51 TraesCS5A01G214400 chrUn 92.784 97 7 0 4213 4309 15904017 15903921 2.390000e-29 141.0
52 TraesCS5A01G214400 chr4B 90.476 105 9 1 4213 4316 511163805 511163701 3.090000e-28 137.0
53 TraesCS5A01G214400 chr4B 94.737 38 2 0 2050 2087 390663580 390663617 6.880000e-05 60.2


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 TraesCS5A01G214400 chr5A 429980067 429986416 6349 False 11727.000000 11727 100.000000 1 6350 1 chr5A.!!$F2 6349
1 TraesCS5A01G214400 chr5A 583623200 583623859 659 True 1086.000000 1086 96.369000 1 661 1 chr5A.!!$R1 660
2 TraesCS5A01G214400 chr5D 326456223 326461428 5205 True 8342.000000 8342 95.621000 692 5899 1 chr5D.!!$R1 5207
3 TraesCS5A01G214400 chr5B 378997156 379002477 5321 True 4004.000000 5845 93.146000 704 6201 2 chr5B.!!$R3 5497
4 TraesCS5A01G214400 chr5B 314976538 314977197 659 False 505.000000 505 80.514000 1 661 1 chr5B.!!$F2 660
5 TraesCS5A01G214400 chr6D 411190187 411194286 4099 True 891.250000 2294 84.633500 1255 5383 4 chr6D.!!$R1 4128
6 TraesCS5A01G214400 chr6A 120116549 120117208 659 True 1120.000000 1120 97.277000 1 661 1 chr6A.!!$R1 660
7 TraesCS5A01G214400 chr6A 555930859 555935083 4224 True 674.166667 1306 85.668333 1001 5510 6 chr6A.!!$R2 4509
8 TraesCS5A01G214400 chr6B 617979345 617984179 4834 True 828.200000 1267 84.688600 1001 5723 5 chr6B.!!$R1 4722
9 TraesCS5A01G214400 chr6B 546088871 546089517 646 False 438.000000 438 78.963000 1 656 1 chr6B.!!$F2 655
10 TraesCS5A01G214400 chr2A 478903328 478903988 660 True 1070.000000 1070 95.921000 2 661 1 chr2A.!!$R2 659
11 TraesCS5A01G214400 chr2D 190432226 190432884 658 False 1053.000000 1053 95.461000 1 661 1 chr2D.!!$F2 660
12 TraesCS5A01G214400 chr2D 650975431 650976090 659 False 1042.000000 1042 95.166000 1 661 1 chr2D.!!$F3 660
13 TraesCS5A01G214400 chr2D 241694531 241695195 664 True 688.000000 688 85.329000 1 668 1 chr2D.!!$R1 667
14 TraesCS5A01G214400 chr3A 632541123 632541780 657 True 1018.000000 1018 94.554000 1 661 1 chr3A.!!$R1 660
15 TraesCS5A01G214400 chr1B 527623611 527624265 654 False 946.000000 946 92.716000 1 658 1 chr1B.!!$F1 657
16 TraesCS5A01G214400 chr1B 293588807 293589455 648 True 872.000000 872 90.854000 1 656 1 chr1B.!!$R1 655
17 TraesCS5A01G214400 chr7D 492774899 492775546 647 False 869.000000 869 90.744000 1 659 1 chr7D.!!$F1 658
18 TraesCS5A01G214400 chr2B 658203513 658204168 655 False 808.000000 808 88.923000 1 656 1 chr2B.!!$F1 655
19 TraesCS5A01G214400 chr7A 427541448 427541955 507 False 767.000000 767 93.910000 153 661 1 chr7A.!!$F1 508
20 TraesCS5A01G214400 chr3D 560261778 560262431 653 True 688.000000 688 85.628000 1 661 1 chr3D.!!$R3 660
21 TraesCS5A01G214400 chr7B 183577093 183577751 658 True 649.000000 649 84.488000 1 661 1 chr7B.!!$R2 660
22 TraesCS5A01G214400 chr7B 609889263 609889815 552 True 597.000000 597 86.126000 1 555 1 chr7B.!!$R3 554

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
684 702 0.603707 GCTTCCTTTTTGCAAGGGGC 60.604 55.000 0.00 2.92 45.13 5.80 F
952 973 0.793617 TCTCCTCCCAGAAACCTCCT 59.206 55.000 0.00 0.00 0.00 3.69 F
1240 1280 1.076995 CCGATTTCCCCCAAGACCC 60.077 63.158 0.00 0.00 0.00 4.46 F
1712 1772 1.884926 CTCTTCTTCCGGGCGATGC 60.885 63.158 0.00 0.00 0.00 3.91 F
2309 2682 1.888512 CAATAAGTGCCAGCCAAGTGT 59.111 47.619 0.00 0.00 0.00 3.55 F
3547 4011 2.350522 CAAGTACATCAGTCTGGTGGC 58.649 52.381 17.42 9.51 31.38 5.01 F
4454 5101 3.544698 TCTTGTCTTGTACTCCCTCCT 57.455 47.619 0.00 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1546 0.975135 TATCGAACACGTCCCCCAAA 59.025 50.000 0.00 0.0 0.00 3.28 R
2011 2368 1.585267 GCCGTGCCATGACACAATCA 61.585 55.000 12.86 0.0 43.13 2.57 R
2100 2471 2.978946 GCTCAAACGGGATGGGGGA 61.979 63.158 0.00 0.0 0.00 4.81 R
3637 4101 1.002430 TGCTTCATCTCGCTTCCAGTT 59.998 47.619 0.00 0.0 0.00 3.16 R
3639 4103 1.134877 TCTGCTTCATCTCGCTTCCAG 60.135 52.381 0.00 0.0 0.00 3.86 R
5085 5966 2.437281 TCCAATCAGGATCTTGCTCTCC 59.563 50.000 0.00 0.0 43.07 3.71 R
6302 7560 0.033920 CAGTTTGGAAGGCTTTGGGC 59.966 55.000 0.00 0.0 40.90 5.36 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
369 375 4.343231 ACACCATTGTCATCCAGCAATTA 58.657 39.130 0.00 0.00 33.55 1.40
661 679 3.853330 CGCATTCACCGCTCGTGG 61.853 66.667 1.46 0.00 43.23 4.94
663 681 2.456119 GCATTCACCGCTCGTGGAG 61.456 63.158 3.09 0.00 43.23 3.86
664 682 1.079819 CATTCACCGCTCGTGGAGT 60.080 57.895 3.09 0.00 43.23 3.85
665 683 1.079819 ATTCACCGCTCGTGGAGTG 60.080 57.895 3.09 0.00 43.23 3.51
666 684 3.858868 TTCACCGCTCGTGGAGTGC 62.859 63.158 3.09 0.00 43.23 4.40
667 685 4.363990 CACCGCTCGTGGAGTGCT 62.364 66.667 3.09 0.00 38.67 4.40
668 686 3.616721 ACCGCTCGTGGAGTGCTT 61.617 61.111 3.09 0.00 38.67 3.91
669 687 2.811317 CCGCTCGTGGAGTGCTTC 60.811 66.667 0.75 0.00 38.67 3.86
670 688 2.811317 CGCTCGTGGAGTGCTTCC 60.811 66.667 1.34 1.34 46.98 3.46
671 689 2.659610 GCTCGTGGAGTGCTTCCT 59.340 61.111 8.90 0.00 46.92 3.36
672 690 1.004440 GCTCGTGGAGTGCTTCCTT 60.004 57.895 8.90 0.00 46.92 3.36
673 691 0.603975 GCTCGTGGAGTGCTTCCTTT 60.604 55.000 8.90 0.00 46.92 3.11
674 692 1.884235 CTCGTGGAGTGCTTCCTTTT 58.116 50.000 8.90 0.00 46.92 2.27
675 693 2.222027 CTCGTGGAGTGCTTCCTTTTT 58.778 47.619 8.90 0.00 46.92 1.94
676 694 1.946768 TCGTGGAGTGCTTCCTTTTTG 59.053 47.619 8.90 0.00 46.92 2.44
677 695 1.600413 CGTGGAGTGCTTCCTTTTTGC 60.600 52.381 8.90 0.00 46.92 3.68
678 696 1.408702 GTGGAGTGCTTCCTTTTTGCA 59.591 47.619 8.90 0.00 46.92 4.08
679 697 2.106566 TGGAGTGCTTCCTTTTTGCAA 58.893 42.857 0.00 0.00 46.92 4.08
680 698 2.101249 TGGAGTGCTTCCTTTTTGCAAG 59.899 45.455 0.00 0.00 46.92 4.01
681 699 2.546584 GGAGTGCTTCCTTTTTGCAAGG 60.547 50.000 0.00 0.00 43.16 3.61
682 700 1.413812 AGTGCTTCCTTTTTGCAAGGG 59.586 47.619 0.00 4.07 38.50 3.95
683 701 0.758123 TGCTTCCTTTTTGCAAGGGG 59.242 50.000 0.00 3.70 37.99 4.79
684 702 0.603707 GCTTCCTTTTTGCAAGGGGC 60.604 55.000 0.00 2.92 45.13 5.80
785 804 8.167605 TGAAAACAAATTAATCAGTAACGGGA 57.832 30.769 0.00 0.00 0.00 5.14
798 817 4.215399 CAGTAACGGGAGATCTTTTTGCAA 59.785 41.667 0.00 0.00 0.00 4.08
946 967 1.626350 CCCCATCTCTCCTCCCAGAAA 60.626 57.143 0.00 0.00 0.00 2.52
948 969 1.488393 CCATCTCTCCTCCCAGAAACC 59.512 57.143 0.00 0.00 0.00 3.27
949 970 2.476199 CATCTCTCCTCCCAGAAACCT 58.524 52.381 0.00 0.00 0.00 3.50
950 971 2.239681 TCTCTCCTCCCAGAAACCTC 57.760 55.000 0.00 0.00 0.00 3.85
951 972 1.199615 CTCTCCTCCCAGAAACCTCC 58.800 60.000 0.00 0.00 0.00 4.30
952 973 0.793617 TCTCCTCCCAGAAACCTCCT 59.206 55.000 0.00 0.00 0.00 3.69
953 974 1.199615 CTCCTCCCAGAAACCTCCTC 58.800 60.000 0.00 0.00 0.00 3.71
954 975 0.793617 TCCTCCCAGAAACCTCCTCT 59.206 55.000 0.00 0.00 0.00 3.69
955 976 1.152271 TCCTCCCAGAAACCTCCTCTT 59.848 52.381 0.00 0.00 0.00 2.85
956 977 1.557371 CCTCCCAGAAACCTCCTCTTC 59.443 57.143 0.00 0.00 0.00 2.87
957 978 2.545810 CTCCCAGAAACCTCCTCTTCT 58.454 52.381 0.00 0.00 31.99 2.85
960 981 2.026729 CCCAGAAACCTCCTCTTCTTCC 60.027 54.545 0.00 0.00 29.29 3.46
1196 1229 1.855690 TACCCTCCCCCTCCCCAATT 61.856 60.000 0.00 0.00 0.00 2.32
1226 1259 3.470888 CTTCGTCCCTGCCCCGAT 61.471 66.667 0.00 0.00 0.00 4.18
1240 1280 1.076995 CCGATTTCCCCCAAGACCC 60.077 63.158 0.00 0.00 0.00 4.46
1712 1772 1.884926 CTCTTCTTCCGGGCGATGC 60.885 63.158 0.00 0.00 0.00 3.91
1782 1848 8.939929 TCATCATAGTTCAACTCTTTCAATGTC 58.060 33.333 0.00 0.00 0.00 3.06
1785 1851 7.388776 TCATAGTTCAACTCTTTCAATGTCCAG 59.611 37.037 0.00 0.00 0.00 3.86
1872 1947 6.881065 TCTCTAGGCATGCCATTGTATAATTC 59.119 38.462 37.18 6.57 38.92 2.17
1905 1980 8.281531 TGATTAATTCAGGTTGAGGATACCAAT 58.718 33.333 0.00 0.00 38.16 3.16
2011 2368 6.183360 TGCATTTCCACTTGAACCATTTACTT 60.183 34.615 0.00 0.00 31.05 2.24
2088 2459 5.401531 TCCGTCCCATATTACAATAGCTC 57.598 43.478 0.00 0.00 0.00 4.09
2169 2542 4.039124 TCAAATTGTTCTTTGGCCCTTCTC 59.961 41.667 0.00 0.00 36.87 2.87
2309 2682 1.888512 CAATAAGTGCCAGCCAAGTGT 59.111 47.619 0.00 0.00 0.00 3.55
2553 2928 4.621068 ATGTACCATGAGCAATTGAACG 57.379 40.909 10.34 0.00 0.00 3.95
2870 3258 3.215151 TCTGCACGGTGTTCCATTTTTA 58.785 40.909 10.24 0.00 0.00 1.52
2871 3259 3.632604 TCTGCACGGTGTTCCATTTTTAA 59.367 39.130 10.24 0.00 0.00 1.52
3023 3411 3.242870 GCAGTTCAAGGCAATATTCGGAG 60.243 47.826 0.00 0.00 0.00 4.63
3182 3583 5.413309 ACTGGTAGATCTTCTCCACAAAG 57.587 43.478 0.00 0.00 0.00 2.77
3547 4011 2.350522 CAAGTACATCAGTCTGGTGGC 58.649 52.381 17.42 9.51 31.38 5.01
3637 4101 3.797039 GCTGTCTGCAGATATGGTTACA 58.203 45.455 21.47 9.99 45.28 2.41
3639 4103 4.034510 GCTGTCTGCAGATATGGTTACAAC 59.965 45.833 21.47 2.61 45.28 3.32
4081 4555 7.068839 TGTCACACACATAACCCTTTTAACAAT 59.931 33.333 0.00 0.00 0.00 2.71
4454 5101 3.544698 TCTTGTCTTGTACTCCCTCCT 57.455 47.619 0.00 0.00 0.00 3.69
4526 5173 7.192232 GGAGCAAAATGAATGAATCTACACTC 58.808 38.462 0.00 0.00 0.00 3.51
5085 5966 2.618709 AGAAGTGCGAGGAAAACCAAAG 59.381 45.455 0.00 0.00 0.00 2.77
5088 5969 1.266989 GTGCGAGGAAAACCAAAGGAG 59.733 52.381 0.00 0.00 0.00 3.69
5092 5973 2.810400 CGAGGAAAACCAAAGGAGAGCA 60.810 50.000 0.00 0.00 0.00 4.26
5265 6398 6.544197 TGCTTATTAACTTTGTCTTGTCCACA 59.456 34.615 0.00 0.00 0.00 4.17
5293 6432 8.396390 GCCTGTGCTAATATGAATTATGATCTG 58.604 37.037 0.00 0.00 33.53 2.90
5415 6614 8.903570 CGAAGCATGTTTATTTGTGGTTATAA 57.096 30.769 0.00 0.00 33.02 0.98
5544 6760 3.430790 CCATTTCTATGCAGTCTCCGTCA 60.431 47.826 0.00 0.00 0.00 4.35
5577 6814 4.043168 GTGGTTCACACGACCCTG 57.957 61.111 0.00 0.00 40.85 4.45
5634 6871 4.281941 AGAAAAGAATCAAGGGCTTCCAAC 59.718 41.667 0.00 0.00 0.00 3.77
5674 6920 0.984230 TCATTCTGAAGCCCGTCCTT 59.016 50.000 0.00 0.00 0.00 3.36
5720 6966 7.917597 ACTGTGTAGACTACTATACAACATCG 58.082 38.462 13.67 1.50 45.22 3.84
5745 6991 7.169140 CGTAGTTTTTCTTTTTGAAATGGAGGG 59.831 37.037 0.00 0.00 43.34 4.30
5746 6992 5.822519 AGTTTTTCTTTTTGAAATGGAGGGC 59.177 36.000 0.00 0.00 43.34 5.19
5750 6996 5.565455 TCTTTTTGAAATGGAGGGCAAAT 57.435 34.783 0.00 0.00 31.20 2.32
5816 7062 6.403049 ACAACACATCGATACTACAAATGGA 58.597 36.000 0.00 0.00 0.00 3.41
5828 7074 5.990668 ACTACAAATGGACATTACTCTCCC 58.009 41.667 0.00 0.00 0.00 4.30
5861 7107 1.142748 CAACTTTTTGGCGCCCACA 59.857 52.632 26.77 2.03 30.78 4.17
5864 7110 1.007387 CTTTTTGGCGCCCACAGTC 60.007 57.895 26.77 0.00 30.78 3.51
5881 7127 2.262915 CACCCAGACTGTCGCCTC 59.737 66.667 1.52 0.00 0.00 4.70
5899 7145 2.031157 CCTCGGTTTTGATGTTGTGGAC 60.031 50.000 0.00 0.00 0.00 4.02
5912 7164 2.365635 TGGACTGCTAGAGGGGCC 60.366 66.667 0.00 0.00 0.00 5.80
5936 7188 3.540314 TTTTGGCAAAAGACACAGCAT 57.460 38.095 20.81 0.00 0.00 3.79
5939 7191 3.096489 TGGCAAAAGACACAGCATTTC 57.904 42.857 0.00 0.00 0.00 2.17
5940 7192 2.694628 TGGCAAAAGACACAGCATTTCT 59.305 40.909 0.00 0.00 0.00 2.52
5941 7193 3.243501 TGGCAAAAGACACAGCATTTCTC 60.244 43.478 0.00 0.00 0.00 2.87
5942 7194 3.005155 GGCAAAAGACACAGCATTTCTCT 59.995 43.478 0.00 0.00 0.00 3.10
5944 7196 4.791974 CAAAAGACACAGCATTTCTCTCC 58.208 43.478 0.00 0.00 0.00 3.71
5962 7218 8.818622 TTCTCTCCTTTCAAATGATTGATGAT 57.181 30.769 0.00 0.00 44.70 2.45
5992 7250 1.447140 GAGCGTGGCCATCGTTGTA 60.447 57.895 22.72 0.00 0.00 2.41
6049 7307 2.691409 TCTTTGGCGGAGTGGATAAG 57.309 50.000 0.00 0.00 0.00 1.73
6062 7320 5.129485 GGAGTGGATAAGGTCTCAAGATGAA 59.871 44.000 0.00 0.00 0.00 2.57
6081 7339 6.382570 AGATGAAGTGTCTAGATGCCTAAGTT 59.617 38.462 0.00 0.00 0.00 2.66
6092 7350 2.257207 TGCCTAAGTTGTAGCCACTCT 58.743 47.619 0.00 0.00 0.00 3.24
6109 7367 4.523943 CCACTCTTTGATCATGTCCCAAAA 59.476 41.667 0.00 0.00 30.56 2.44
6111 7369 5.242393 CACTCTTTGATCATGTCCCAAAACT 59.758 40.000 0.00 0.00 30.56 2.66
6114 7372 7.505585 ACTCTTTGATCATGTCCCAAAACTTAA 59.494 33.333 0.00 0.00 30.56 1.85
6115 7373 8.421249 TCTTTGATCATGTCCCAAAACTTAAT 57.579 30.769 0.00 0.00 30.56 1.40
6116 7374 8.522830 TCTTTGATCATGTCCCAAAACTTAATC 58.477 33.333 0.00 0.00 30.56 1.75
6117 7375 6.435430 TGATCATGTCCCAAAACTTAATCG 57.565 37.500 0.00 0.00 0.00 3.34
6118 7376 5.943416 TGATCATGTCCCAAAACTTAATCGT 59.057 36.000 0.00 0.00 0.00 3.73
6140 7398 7.977904 TCGTATATCGACACTTGTAGAAAAGA 58.022 34.615 0.00 0.00 44.01 2.52
6147 7405 5.465390 CGACACTTGTAGAAAAGATGGTCAA 59.535 40.000 0.00 0.00 31.77 3.18
6160 7418 6.927294 AAGATGGTCAACGGATTCTTTATC 57.073 37.500 0.00 0.00 0.00 1.75
6180 7438 1.718757 GCGCTTGCATAGGGGACAAG 61.719 60.000 0.00 0.00 42.90 3.16
6181 7439 1.097547 CGCTTGCATAGGGGACAAGG 61.098 60.000 0.00 0.00 40.87 3.61
6201 7459 3.615224 GGCAACAATTTGACCATCCAT 57.385 42.857 2.79 0.00 34.18 3.41
6202 7460 4.734398 GGCAACAATTTGACCATCCATA 57.266 40.909 2.79 0.00 34.18 2.74
6203 7461 4.432712 GGCAACAATTTGACCATCCATAC 58.567 43.478 2.79 0.00 34.18 2.39
6204 7462 4.160252 GGCAACAATTTGACCATCCATACT 59.840 41.667 2.79 0.00 34.18 2.12
6205 7463 5.337491 GGCAACAATTTGACCATCCATACTT 60.337 40.000 2.79 0.00 34.18 2.24
6206 7464 6.165577 GCAACAATTTGACCATCCATACTTT 58.834 36.000 2.79 0.00 34.24 2.66
6207 7465 6.650390 GCAACAATTTGACCATCCATACTTTT 59.350 34.615 2.79 0.00 34.24 2.27
6208 7466 7.173047 GCAACAATTTGACCATCCATACTTTTT 59.827 33.333 2.79 0.00 34.24 1.94
6230 7488 4.819105 TTTTGAGACGACCATCCATACT 57.181 40.909 0.00 0.00 0.00 2.12
6231 7489 4.819105 TTTGAGACGACCATCCATACTT 57.181 40.909 0.00 0.00 0.00 2.24
6232 7490 3.801114 TGAGACGACCATCCATACTTG 57.199 47.619 0.00 0.00 0.00 3.16
6233 7491 2.430694 TGAGACGACCATCCATACTTGG 59.569 50.000 0.00 0.00 45.15 3.61
6234 7492 1.139058 AGACGACCATCCATACTTGGC 59.861 52.381 0.00 0.00 43.29 4.52
6235 7493 0.180406 ACGACCATCCATACTTGGCC 59.820 55.000 0.00 0.00 43.29 5.36
6236 7494 0.180171 CGACCATCCATACTTGGCCA 59.820 55.000 0.00 0.00 43.29 5.36
6237 7495 1.408127 CGACCATCCATACTTGGCCAA 60.408 52.381 19.25 19.25 43.29 4.52
6238 7496 2.024414 GACCATCCATACTTGGCCAAC 58.976 52.381 16.05 0.00 43.29 3.77
6239 7497 1.640670 ACCATCCATACTTGGCCAACT 59.359 47.619 16.05 8.64 43.29 3.16
6240 7498 2.026641 CCATCCATACTTGGCCAACTG 58.973 52.381 16.05 12.18 43.29 3.16
6241 7499 2.357050 CCATCCATACTTGGCCAACTGA 60.357 50.000 16.05 7.08 43.29 3.41
6242 7500 3.559069 CATCCATACTTGGCCAACTGAT 58.441 45.455 16.05 9.12 43.29 2.90
6243 7501 3.281727 TCCATACTTGGCCAACTGATC 57.718 47.619 16.05 0.00 43.29 2.92
6244 7502 2.092429 TCCATACTTGGCCAACTGATCC 60.092 50.000 16.05 0.00 43.29 3.36
6245 7503 2.092212 CCATACTTGGCCAACTGATCCT 60.092 50.000 16.05 0.00 35.85 3.24
6246 7504 3.209410 CATACTTGGCCAACTGATCCTC 58.791 50.000 16.05 0.00 0.00 3.71
6247 7505 0.036010 ACTTGGCCAACTGATCCTCG 60.036 55.000 16.05 3.84 0.00 4.63
6248 7506 0.745845 CTTGGCCAACTGATCCTCGG 60.746 60.000 16.05 0.00 0.00 4.63
6249 7507 1.488705 TTGGCCAACTGATCCTCGGT 61.489 55.000 16.05 0.00 37.65 4.69
6250 7508 1.299976 GGCCAACTGATCCTCGGTT 59.700 57.895 0.00 0.00 46.17 4.44
6251 7509 0.744771 GGCCAACTGATCCTCGGTTC 60.745 60.000 0.00 0.00 43.61 3.62
6252 7510 0.036388 GCCAACTGATCCTCGGTTCA 60.036 55.000 0.00 0.00 43.61 3.18
6253 7511 1.610624 GCCAACTGATCCTCGGTTCAA 60.611 52.381 0.00 0.00 43.61 2.69
6254 7512 2.778299 CCAACTGATCCTCGGTTCAAA 58.222 47.619 0.00 0.00 43.61 2.69
6255 7513 3.347216 CCAACTGATCCTCGGTTCAAAT 58.653 45.455 0.00 0.00 43.61 2.32
6256 7514 3.375299 CCAACTGATCCTCGGTTCAAATC 59.625 47.826 0.00 0.00 43.61 2.17
6257 7515 3.268023 ACTGATCCTCGGTTCAAATCC 57.732 47.619 0.00 0.00 30.35 3.01
6258 7516 2.840651 ACTGATCCTCGGTTCAAATCCT 59.159 45.455 0.00 0.00 30.35 3.24
6259 7517 4.030913 ACTGATCCTCGGTTCAAATCCTA 58.969 43.478 0.00 0.00 30.35 2.94
6260 7518 4.656112 ACTGATCCTCGGTTCAAATCCTAT 59.344 41.667 0.00 0.00 30.35 2.57
6261 7519 5.131142 ACTGATCCTCGGTTCAAATCCTATT 59.869 40.000 0.00 0.00 30.35 1.73
6262 7520 6.001449 TGATCCTCGGTTCAAATCCTATTT 57.999 37.500 0.00 0.00 0.00 1.40
6263 7521 6.423182 TGATCCTCGGTTCAAATCCTATTTT 58.577 36.000 0.00 0.00 0.00 1.82
6264 7522 6.318648 TGATCCTCGGTTCAAATCCTATTTTG 59.681 38.462 0.00 0.00 37.83 2.44
6265 7523 5.566469 TCCTCGGTTCAAATCCTATTTTGT 58.434 37.500 0.00 0.00 37.73 2.83
6266 7524 6.713276 TCCTCGGTTCAAATCCTATTTTGTA 58.287 36.000 0.00 0.00 37.73 2.41
6267 7525 7.343357 TCCTCGGTTCAAATCCTATTTTGTAT 58.657 34.615 0.00 0.00 37.73 2.29
6268 7526 7.282224 TCCTCGGTTCAAATCCTATTTTGTATG 59.718 37.037 0.00 0.00 37.73 2.39
6269 7527 7.328277 TCGGTTCAAATCCTATTTTGTATGG 57.672 36.000 0.00 0.00 37.73 2.74
6270 7528 5.977129 CGGTTCAAATCCTATTTTGTATGGC 59.023 40.000 0.00 0.00 37.73 4.40
6271 7529 6.405286 CGGTTCAAATCCTATTTTGTATGGCA 60.405 38.462 0.00 0.00 37.73 4.92
6272 7530 7.327214 GGTTCAAATCCTATTTTGTATGGCAA 58.673 34.615 0.00 0.00 37.73 4.52
6273 7531 7.492344 GGTTCAAATCCTATTTTGTATGGCAAG 59.508 37.037 0.00 0.00 38.47 4.01
6274 7532 6.572519 TCAAATCCTATTTTGTATGGCAAGC 58.427 36.000 0.00 0.00 38.47 4.01
6275 7533 6.154192 TCAAATCCTATTTTGTATGGCAAGCA 59.846 34.615 0.00 0.00 38.47 3.91
6276 7534 6.543430 AATCCTATTTTGTATGGCAAGCAA 57.457 33.333 0.00 0.00 38.47 3.91
6277 7535 5.991933 TCCTATTTTGTATGGCAAGCAAA 57.008 34.783 13.39 13.39 38.47 3.68
6278 7536 5.719173 TCCTATTTTGTATGGCAAGCAAAC 58.281 37.500 15.96 1.11 38.47 2.93
6279 7537 5.480073 TCCTATTTTGTATGGCAAGCAAACT 59.520 36.000 15.96 13.89 38.47 2.66
6280 7538 5.577945 CCTATTTTGTATGGCAAGCAAACTG 59.422 40.000 15.96 10.52 38.47 3.16
6281 7539 4.662468 TTTTGTATGGCAAGCAAACTGA 57.338 36.364 15.96 3.63 38.47 3.41
6282 7540 4.662468 TTTGTATGGCAAGCAAACTGAA 57.338 36.364 13.39 0.00 38.47 3.02
6283 7541 3.921119 TGTATGGCAAGCAAACTGAAG 57.079 42.857 0.00 0.00 0.00 3.02
6284 7542 3.485394 TGTATGGCAAGCAAACTGAAGA 58.515 40.909 0.00 0.00 0.00 2.87
6285 7543 3.888323 TGTATGGCAAGCAAACTGAAGAA 59.112 39.130 0.00 0.00 0.00 2.52
6286 7544 4.523943 TGTATGGCAAGCAAACTGAAGAAT 59.476 37.500 0.00 0.00 0.00 2.40
6287 7545 4.612264 ATGGCAAGCAAACTGAAGAATT 57.388 36.364 0.00 0.00 0.00 2.17
6288 7546 4.405116 TGGCAAGCAAACTGAAGAATTT 57.595 36.364 0.00 0.00 0.00 1.82
6289 7547 5.528043 TGGCAAGCAAACTGAAGAATTTA 57.472 34.783 0.00 0.00 0.00 1.40
6290 7548 5.911752 TGGCAAGCAAACTGAAGAATTTAA 58.088 33.333 0.00 0.00 0.00 1.52
6291 7549 6.523840 TGGCAAGCAAACTGAAGAATTTAAT 58.476 32.000 0.00 0.00 0.00 1.40
6292 7550 6.646240 TGGCAAGCAAACTGAAGAATTTAATC 59.354 34.615 0.00 0.00 0.00 1.75
6293 7551 6.870439 GGCAAGCAAACTGAAGAATTTAATCT 59.130 34.615 0.00 0.00 0.00 2.40
6294 7552 7.386025 GGCAAGCAAACTGAAGAATTTAATCTT 59.614 33.333 0.00 0.00 42.24 2.40
6295 7553 8.219105 GCAAGCAAACTGAAGAATTTAATCTTG 58.781 33.333 0.00 0.00 39.70 3.02
6296 7554 9.467258 CAAGCAAACTGAAGAATTTAATCTTGA 57.533 29.630 0.00 0.00 39.70 3.02
6297 7555 9.688592 AAGCAAACTGAAGAATTTAATCTTGAG 57.311 29.630 4.36 4.36 43.60 3.02
6298 7556 9.071276 AGCAAACTGAAGAATTTAATCTTGAGA 57.929 29.630 10.95 0.00 41.46 3.27
6299 7557 9.339492 GCAAACTGAAGAATTTAATCTTGAGAG 57.661 33.333 10.95 3.86 41.46 3.20
6300 7558 9.837525 CAAACTGAAGAATTTAATCTTGAGAGG 57.162 33.333 10.95 0.00 41.46 3.69
6301 7559 9.799106 AAACTGAAGAATTTAATCTTGAGAGGA 57.201 29.630 10.95 0.00 41.46 3.71
6302 7560 9.447157 AACTGAAGAATTTAATCTTGAGAGGAG 57.553 33.333 10.95 0.00 41.46 3.69
6303 7561 7.552330 ACTGAAGAATTTAATCTTGAGAGGAGC 59.448 37.037 10.95 0.00 41.46 4.70
6304 7562 6.825721 TGAAGAATTTAATCTTGAGAGGAGCC 59.174 38.462 0.00 0.00 39.70 4.70
6305 7563 5.689835 AGAATTTAATCTTGAGAGGAGCCC 58.310 41.667 0.00 0.00 0.00 5.19
6306 7564 5.192522 AGAATTTAATCTTGAGAGGAGCCCA 59.807 40.000 0.00 0.00 0.00 5.36
6307 7565 4.927267 TTTAATCTTGAGAGGAGCCCAA 57.073 40.909 0.00 0.00 0.00 4.12
6308 7566 4.927267 TTAATCTTGAGAGGAGCCCAAA 57.073 40.909 0.00 0.00 0.00 3.28
6309 7567 3.362870 AATCTTGAGAGGAGCCCAAAG 57.637 47.619 0.00 0.00 0.00 2.77
6310 7568 0.326264 TCTTGAGAGGAGCCCAAAGC 59.674 55.000 0.00 0.00 44.25 3.51
6311 7569 0.679321 CTTGAGAGGAGCCCAAAGCC 60.679 60.000 0.00 0.00 45.47 4.35
6312 7570 1.136329 TTGAGAGGAGCCCAAAGCCT 61.136 55.000 0.00 0.00 45.47 4.58
6313 7571 1.136329 TGAGAGGAGCCCAAAGCCTT 61.136 55.000 0.00 0.00 45.47 4.35
6314 7572 0.393673 GAGAGGAGCCCAAAGCCTTC 60.394 60.000 0.00 0.00 45.47 3.46
6315 7573 1.379176 GAGGAGCCCAAAGCCTTCC 60.379 63.158 0.00 0.00 45.47 3.46
6316 7574 2.142292 GAGGAGCCCAAAGCCTTCCA 62.142 60.000 0.00 0.00 45.47 3.53
6317 7575 1.228862 GGAGCCCAAAGCCTTCCAA 60.229 57.895 0.00 0.00 45.47 3.53
6318 7576 0.831711 GGAGCCCAAAGCCTTCCAAA 60.832 55.000 0.00 0.00 45.47 3.28
6319 7577 0.318441 GAGCCCAAAGCCTTCCAAAC 59.682 55.000 0.00 0.00 45.47 2.93
6320 7578 0.105504 AGCCCAAAGCCTTCCAAACT 60.106 50.000 0.00 0.00 45.47 2.66
6321 7579 0.033920 GCCCAAAGCCTTCCAAACTG 59.966 55.000 0.00 0.00 34.35 3.16
6322 7580 1.413118 CCCAAAGCCTTCCAAACTGT 58.587 50.000 0.00 0.00 0.00 3.55
6323 7581 1.069049 CCCAAAGCCTTCCAAACTGTG 59.931 52.381 0.00 0.00 0.00 3.66
6324 7582 1.756538 CCAAAGCCTTCCAAACTGTGT 59.243 47.619 0.00 0.00 0.00 3.72
6325 7583 2.481795 CCAAAGCCTTCCAAACTGTGTG 60.482 50.000 0.00 0.00 0.00 3.82
6326 7584 0.746659 AAGCCTTCCAAACTGTGTGC 59.253 50.000 0.00 0.00 0.00 4.57
6327 7585 0.106519 AGCCTTCCAAACTGTGTGCT 60.107 50.000 0.00 0.00 0.00 4.40
6328 7586 0.312102 GCCTTCCAAACTGTGTGCTC 59.688 55.000 0.00 0.00 0.00 4.26
6329 7587 0.954452 CCTTCCAAACTGTGTGCTCC 59.046 55.000 0.00 0.00 0.00 4.70
6330 7588 1.679139 CTTCCAAACTGTGTGCTCCA 58.321 50.000 0.00 0.00 0.00 3.86
6331 7589 2.233271 CTTCCAAACTGTGTGCTCCAT 58.767 47.619 0.00 0.00 0.00 3.41
6332 7590 1.608055 TCCAAACTGTGTGCTCCATG 58.392 50.000 0.00 0.00 0.00 3.66
6333 7591 1.142667 TCCAAACTGTGTGCTCCATGA 59.857 47.619 0.00 0.00 0.00 3.07
6334 7592 1.538512 CCAAACTGTGTGCTCCATGAG 59.461 52.381 0.00 0.00 0.00 2.90
6335 7593 1.538512 CAAACTGTGTGCTCCATGAGG 59.461 52.381 0.00 0.00 0.00 3.86
6336 7594 0.037303 AACTGTGTGCTCCATGAGGG 59.963 55.000 0.00 0.00 34.83 4.30
6337 7595 0.837691 ACTGTGTGCTCCATGAGGGA 60.838 55.000 0.00 0.00 45.89 4.20
6347 7605 3.370840 TCCATGAGGGAACAAATGGAG 57.629 47.619 0.00 0.00 44.81 3.86
6348 7606 1.753073 CCATGAGGGAACAAATGGAGC 59.247 52.381 0.00 0.00 44.28 4.70
6349 7607 2.622452 CCATGAGGGAACAAATGGAGCT 60.622 50.000 0.00 0.00 44.28 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 7.178628 GTGAATACTGGCTCTATACCTAATGGA 59.821 40.741 0.00 0.00 37.04 3.41
432 443 4.635765 GTGCAAACTGGCTCTTACATGATA 59.364 41.667 0.00 0.00 34.04 2.15
661 679 2.546584 CCCTTGCAAAAAGGAAGCACTC 60.547 50.000 4.39 0.00 43.63 3.51
663 681 1.541015 CCCCTTGCAAAAAGGAAGCAC 60.541 52.381 4.39 0.00 43.63 4.40
664 682 0.758123 CCCCTTGCAAAAAGGAAGCA 59.242 50.000 4.39 0.00 43.63 3.91
665 683 0.603707 GCCCCTTGCAAAAAGGAAGC 60.604 55.000 12.10 7.48 43.63 3.86
666 684 3.612517 GCCCCTTGCAAAAAGGAAG 57.387 52.632 12.10 1.87 44.48 3.46
676 694 1.953231 GCTTCAATCCTGCCCCTTGC 61.953 60.000 0.00 0.00 41.77 4.01
677 695 0.612732 TGCTTCAATCCTGCCCCTTG 60.613 55.000 0.00 0.00 0.00 3.61
678 696 0.324091 CTGCTTCAATCCTGCCCCTT 60.324 55.000 0.00 0.00 0.00 3.95
679 697 1.210204 TCTGCTTCAATCCTGCCCCT 61.210 55.000 0.00 0.00 0.00 4.79
680 698 0.750911 CTCTGCTTCAATCCTGCCCC 60.751 60.000 0.00 0.00 0.00 5.80
681 699 0.750911 CCTCTGCTTCAATCCTGCCC 60.751 60.000 0.00 0.00 0.00 5.36
682 700 0.254178 TCCTCTGCTTCAATCCTGCC 59.746 55.000 0.00 0.00 0.00 4.85
683 701 2.015587 CTTCCTCTGCTTCAATCCTGC 58.984 52.381 0.00 0.00 0.00 4.85
684 702 3.533547 CTCTTCCTCTGCTTCAATCCTG 58.466 50.000 0.00 0.00 0.00 3.86
685 703 2.504996 CCTCTTCCTCTGCTTCAATCCT 59.495 50.000 0.00 0.00 0.00 3.24
686 704 2.503356 TCCTCTTCCTCTGCTTCAATCC 59.497 50.000 0.00 0.00 0.00 3.01
687 705 3.902881 TCCTCTTCCTCTGCTTCAATC 57.097 47.619 0.00 0.00 0.00 2.67
688 706 3.181467 CGATCCTCTTCCTCTGCTTCAAT 60.181 47.826 0.00 0.00 0.00 2.57
689 707 2.167281 CGATCCTCTTCCTCTGCTTCAA 59.833 50.000 0.00 0.00 0.00 2.69
690 708 1.753649 CGATCCTCTTCCTCTGCTTCA 59.246 52.381 0.00 0.00 0.00 3.02
760 779 8.167605 TCCCGTTACTGATTAATTTGTTTTCA 57.832 30.769 0.00 0.00 0.00 2.69
785 804 4.734266 AGGGAGTCTTTGCAAAAAGATCT 58.266 39.130 13.84 7.89 40.50 2.75
798 817 3.852558 CCGGATCCTAGGGAGTCTT 57.147 57.895 9.46 0.00 34.05 3.01
946 967 1.007842 GGAGGAGGAAGAAGAGGAGGT 59.992 57.143 0.00 0.00 0.00 3.85
948 969 2.666317 GAGGAGGAGGAAGAAGAGGAG 58.334 57.143 0.00 0.00 0.00 3.69
949 970 1.289530 GGAGGAGGAGGAAGAAGAGGA 59.710 57.143 0.00 0.00 0.00 3.71
950 971 1.290732 AGGAGGAGGAGGAAGAAGAGG 59.709 57.143 0.00 0.00 0.00 3.69
951 972 2.666317 GAGGAGGAGGAGGAAGAAGAG 58.334 57.143 0.00 0.00 0.00 2.85
952 973 1.289530 GGAGGAGGAGGAGGAAGAAGA 59.710 57.143 0.00 0.00 0.00 2.87
953 974 1.290732 AGGAGGAGGAGGAGGAAGAAG 59.709 57.143 0.00 0.00 0.00 2.85
954 975 1.289530 GAGGAGGAGGAGGAGGAAGAA 59.710 57.143 0.00 0.00 0.00 2.52
955 976 0.930726 GAGGAGGAGGAGGAGGAAGA 59.069 60.000 0.00 0.00 0.00 2.87
956 977 0.467290 CGAGGAGGAGGAGGAGGAAG 60.467 65.000 0.00 0.00 0.00 3.46
957 978 1.615814 CGAGGAGGAGGAGGAGGAA 59.384 63.158 0.00 0.00 0.00 3.36
960 981 2.520741 GGCGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1083 1107 2.364448 AGGGAGGAGGCGAAGGAC 60.364 66.667 0.00 0.00 0.00 3.85
1226 1259 1.151908 CGTTGGGTCTTGGGGGAAA 59.848 57.895 0.00 0.00 0.00 3.13
1240 1280 1.081641 CCTGCAGCAAAGCTCGTTG 60.082 57.895 8.66 0.00 36.40 4.10
1413 1467 2.932614 CACTCCAATCGAGCACCTAAAG 59.067 50.000 0.00 0.00 43.01 1.85
1415 1469 2.176045 TCACTCCAATCGAGCACCTAA 58.824 47.619 0.00 0.00 43.01 2.69
1416 1470 1.847328 TCACTCCAATCGAGCACCTA 58.153 50.000 0.00 0.00 43.01 3.08
1474 1531 1.205064 CAAACTCTCCTGCAACGCG 59.795 57.895 3.53 3.53 0.00 6.01
1489 1546 0.975135 TATCGAACACGTCCCCCAAA 59.025 50.000 0.00 0.00 0.00 3.28
1712 1772 4.020839 ACCCAGAAATTGGCAAATTGAGAG 60.021 41.667 5.05 0.00 46.32 3.20
1782 1848 7.375834 TCAGTTAACACAGATGTAACTACTGG 58.624 38.462 8.61 0.00 38.45 4.00
1785 1851 7.871463 ACCTTCAGTTAACACAGATGTAACTAC 59.129 37.037 8.61 0.00 38.45 2.73
1872 1947 5.698832 TCAACCTGAATTAATCAAACAGCG 58.301 37.500 0.00 0.00 37.67 5.18
1928 2003 2.045885 ACCTCCCCATTCTCCAGTCTTA 59.954 50.000 0.00 0.00 0.00 2.10
2011 2368 1.585267 GCCGTGCCATGACACAATCA 61.585 55.000 12.86 0.00 43.13 2.57
2100 2471 2.978946 GCTCAAACGGGATGGGGGA 61.979 63.158 0.00 0.00 0.00 4.81
2186 2559 7.394359 ACTTTGTCAGCAATAACCTACATGAAT 59.606 33.333 0.00 0.00 34.18 2.57
2553 2928 3.895232 TTGAGGAGTCTTCCATGTAGC 57.105 47.619 0.00 0.00 46.64 3.58
2981 3369 6.938507 ACTGCAAATATCATGACCAAATGTT 58.061 32.000 0.00 0.00 0.00 2.71
2983 3371 7.036829 TGAACTGCAAATATCATGACCAAATG 58.963 34.615 0.00 0.00 0.00 2.32
2984 3372 7.172868 TGAACTGCAAATATCATGACCAAAT 57.827 32.000 0.00 0.00 0.00 2.32
3547 4011 1.063717 ACATACCCTTTGGAGCCATGG 60.064 52.381 7.63 7.63 34.81 3.66
3637 4101 1.002430 TGCTTCATCTCGCTTCCAGTT 59.998 47.619 0.00 0.00 0.00 3.16
3639 4103 1.134877 TCTGCTTCATCTCGCTTCCAG 60.135 52.381 0.00 0.00 0.00 3.86
4049 4520 4.530553 AGGGTTATGTGTGTGACATCTACA 59.469 41.667 0.00 0.00 41.91 2.74
4416 5063 7.431249 AGACAAGAATATTAAATGCATGCCTG 58.569 34.615 16.68 0.00 0.00 4.85
4582 5229 7.321153 CAGATATTCCCTCCGTTACGAAATAT 58.679 38.462 6.24 7.48 0.00 1.28
4590 5237 5.580998 AGATAGCAGATATTCCCTCCGTTA 58.419 41.667 0.00 0.00 0.00 3.18
5034 5915 8.567948 TGAGACATTAGTTGAAAAACAAGGATC 58.432 33.333 0.00 0.00 39.30 3.36
5085 5966 2.437281 TCCAATCAGGATCTTGCTCTCC 59.563 50.000 0.00 0.00 43.07 3.71
5108 5989 8.204160 TCCATAGATAAAGCAAAGATTTCTCGA 58.796 33.333 0.00 0.00 0.00 4.04
5293 6432 4.436242 TCAGATTGAAGTCGACCTGTAC 57.564 45.455 13.01 0.02 0.00 2.90
5415 6614 5.652994 TGCAAAGTACTGGTTTTCAAAGT 57.347 34.783 0.00 0.00 0.00 2.66
5544 6760 5.008613 GTGAACCACAAGATACACAACACAT 59.991 40.000 0.00 0.00 34.08 3.21
5577 6814 1.192534 GTAGGATATTCGCTTGCGTGC 59.807 52.381 14.70 1.03 0.00 5.34
5588 6825 4.829872 TTCCAACCGTGTGTAGGATATT 57.170 40.909 0.00 0.00 0.00 1.28
5660 6906 2.990066 ATAGAAAGGACGGGCTTCAG 57.010 50.000 0.00 0.00 0.00 3.02
5674 6920 1.074084 TGGCCGTGGTTGGAAATAGAA 59.926 47.619 0.00 0.00 0.00 2.10
5731 6977 7.684937 CAAATATTTGCCCTCCATTTCAAAA 57.315 32.000 14.96 0.00 32.97 2.44
5750 6996 9.823647 CTCTCTTAGTTAAAGATGAGGCAAATA 57.176 33.333 0.00 0.00 43.32 1.40
5764 7010 9.730420 GCACAAACAAATTTCTCTCTTAGTTAA 57.270 29.630 0.00 0.00 0.00 2.01
5800 7046 8.234136 AGAGTAATGTCCATTTGTAGTATCGA 57.766 34.615 0.00 0.00 32.50 3.59
5806 7052 5.050490 CGGGAGAGTAATGTCCATTTGTAG 58.950 45.833 8.76 0.00 34.14 2.74
5816 7062 1.496060 TCATGCCGGGAGAGTAATGT 58.504 50.000 2.18 0.00 0.00 2.71
5828 7074 1.176527 AGTTGGGTTCAATCATGCCG 58.823 50.000 0.00 0.00 35.10 5.69
5864 7110 2.262915 GAGGCGACAGTCTGGGTG 59.737 66.667 4.53 0.00 28.74 4.61
5881 7127 2.858260 GCAGTCCACAACATCAAAACCG 60.858 50.000 0.00 0.00 0.00 4.44
5920 7172 3.005155 AGAGAAATGCTGTGTCTTTTGCC 59.995 43.478 0.00 0.00 0.00 4.52
5923 7175 4.723309 AGGAGAGAAATGCTGTGTCTTTT 58.277 39.130 0.00 0.00 0.00 2.27
5932 7184 7.177921 TCAATCATTTGAAAGGAGAGAAATGCT 59.822 33.333 0.00 0.00 38.90 3.79
5933 7185 7.318141 TCAATCATTTGAAAGGAGAGAAATGC 58.682 34.615 0.00 0.00 38.90 3.56
5934 7186 9.302345 CATCAATCATTTGAAAGGAGAGAAATG 57.698 33.333 0.00 0.00 44.70 2.32
5935 7187 9.251440 TCATCAATCATTTGAAAGGAGAGAAAT 57.749 29.630 0.00 0.00 44.70 2.17
5936 7188 8.640063 TCATCAATCATTTGAAAGGAGAGAAA 57.360 30.769 0.00 0.00 44.70 2.52
5939 7191 7.915923 CACATCATCAATCATTTGAAAGGAGAG 59.084 37.037 0.00 0.00 44.70 3.20
5940 7192 7.612633 TCACATCATCAATCATTTGAAAGGAGA 59.387 33.333 0.00 0.00 44.70 3.71
5941 7193 7.768240 TCACATCATCAATCATTTGAAAGGAG 58.232 34.615 0.00 0.00 44.70 3.69
5942 7194 7.629866 GCTCACATCATCAATCATTTGAAAGGA 60.630 37.037 0.00 0.00 44.70 3.36
5944 7196 7.033185 TGCTCACATCATCAATCATTTGAAAG 58.967 34.615 0.00 0.00 44.70 2.62
5962 7218 4.377708 ACGCTCGCCATGCTCACA 62.378 61.111 0.00 0.00 0.00 3.58
5987 7243 2.100087 CACCAACACCCCAAACTACAAC 59.900 50.000 0.00 0.00 0.00 3.32
5992 7250 0.750182 CGACACCAACACCCCAAACT 60.750 55.000 0.00 0.00 0.00 2.66
6042 7300 5.485353 ACACTTCATCTTGAGACCTTATCCA 59.515 40.000 0.00 0.00 0.00 3.41
6049 7307 5.906113 TCTAGACACTTCATCTTGAGACC 57.094 43.478 0.00 0.00 0.00 3.85
6062 7320 5.163499 GCTACAACTTAGGCATCTAGACACT 60.163 44.000 0.00 0.00 0.00 3.55
6081 7339 4.507710 GACATGATCAAAGAGTGGCTACA 58.492 43.478 0.00 0.00 0.00 2.74
6092 7350 7.040062 ACGATTAAGTTTTGGGACATGATCAAA 60.040 33.333 0.00 4.34 39.30 2.69
6116 7374 8.682895 CATCTTTTCTACAAGTGTCGATATACG 58.317 37.037 0.00 0.00 44.09 3.06
6117 7375 8.969267 CCATCTTTTCTACAAGTGTCGATATAC 58.031 37.037 0.00 0.00 0.00 1.47
6118 7376 8.692710 ACCATCTTTTCTACAAGTGTCGATATA 58.307 33.333 0.00 0.00 0.00 0.86
6132 7390 6.049955 AGAATCCGTTGACCATCTTTTCTA 57.950 37.500 0.00 0.00 0.00 2.10
6140 7398 3.560068 GCGATAAAGAATCCGTTGACCAT 59.440 43.478 0.00 0.00 0.00 3.55
6147 7405 1.593006 CAAGCGCGATAAAGAATCCGT 59.407 47.619 12.10 0.00 33.45 4.69
6160 7418 3.272334 GTCCCCTATGCAAGCGCG 61.272 66.667 0.00 0.00 42.97 6.86
6180 7438 1.622811 TGGATGGTCAAATTGTTGCCC 59.377 47.619 0.00 0.00 33.14 5.36
6181 7439 3.615224 ATGGATGGTCAAATTGTTGCC 57.385 42.857 0.00 0.00 34.50 4.52
6208 7466 5.160607 AGTATGGATGGTCGTCTCAAAAA 57.839 39.130 0.00 0.00 0.00 1.94
6209 7467 4.819105 AGTATGGATGGTCGTCTCAAAA 57.181 40.909 0.00 0.00 0.00 2.44
6210 7468 4.503910 CAAGTATGGATGGTCGTCTCAAA 58.496 43.478 0.00 0.00 0.00 2.69
6211 7469 4.123497 CAAGTATGGATGGTCGTCTCAA 57.877 45.455 0.00 0.00 0.00 3.02
6212 7470 3.801114 CAAGTATGGATGGTCGTCTCA 57.199 47.619 0.00 0.00 0.00 3.27
6222 7480 7.447419 GAGGATCAGTTGGCCAAGTATGGAT 62.447 48.000 25.35 21.97 42.15 3.41
6223 7481 6.209457 GAGGATCAGTTGGCCAAGTATGGA 62.209 50.000 25.35 18.39 42.15 3.41
6224 7482 3.995846 GAGGATCAGTTGGCCAAGTATGG 60.996 52.174 25.35 13.63 42.36 2.74
6225 7483 3.209410 GAGGATCAGTTGGCCAAGTATG 58.791 50.000 25.35 19.97 33.17 2.39
6226 7484 2.158900 CGAGGATCAGTTGGCCAAGTAT 60.159 50.000 25.35 17.72 33.17 2.12
6227 7485 1.207089 CGAGGATCAGTTGGCCAAGTA 59.793 52.381 25.35 14.01 33.17 2.24
6228 7486 0.036010 CGAGGATCAGTTGGCCAAGT 60.036 55.000 21.21 20.87 33.17 3.16
6229 7487 0.745845 CCGAGGATCAGTTGGCCAAG 60.746 60.000 21.21 8.63 33.17 3.61
6230 7488 1.299648 CCGAGGATCAGTTGGCCAA 59.700 57.895 16.05 16.05 33.17 4.52
6231 7489 1.488705 AACCGAGGATCAGTTGGCCA 61.489 55.000 0.00 0.00 33.78 5.36
6232 7490 0.744771 GAACCGAGGATCAGTTGGCC 60.745 60.000 0.00 0.00 35.52 5.36
6233 7491 0.036388 TGAACCGAGGATCAGTTGGC 60.036 55.000 0.00 0.00 35.52 4.52
6234 7492 2.472695 TTGAACCGAGGATCAGTTGG 57.527 50.000 2.43 0.00 35.52 3.77
6235 7493 3.375299 GGATTTGAACCGAGGATCAGTTG 59.625 47.826 2.43 0.00 35.52 3.16
6236 7494 3.264450 AGGATTTGAACCGAGGATCAGTT 59.736 43.478 2.43 0.00 38.69 3.16
6237 7495 2.840651 AGGATTTGAACCGAGGATCAGT 59.159 45.455 2.43 0.00 33.17 3.41
6238 7496 3.550437 AGGATTTGAACCGAGGATCAG 57.450 47.619 2.43 0.00 33.17 2.90
6239 7497 5.630415 AATAGGATTTGAACCGAGGATCA 57.370 39.130 0.00 0.00 33.17 2.92
6240 7498 6.318900 ACAAAATAGGATTTGAACCGAGGATC 59.681 38.462 6.76 0.00 41.73 3.36
6241 7499 6.187682 ACAAAATAGGATTTGAACCGAGGAT 58.812 36.000 6.76 0.00 41.73 3.24
6242 7500 5.566469 ACAAAATAGGATTTGAACCGAGGA 58.434 37.500 6.76 0.00 41.73 3.71
6243 7501 5.897377 ACAAAATAGGATTTGAACCGAGG 57.103 39.130 6.76 0.00 41.73 4.63
6244 7502 7.417612 CCATACAAAATAGGATTTGAACCGAG 58.582 38.462 6.76 0.00 41.73 4.63
6245 7503 6.183360 GCCATACAAAATAGGATTTGAACCGA 60.183 38.462 6.76 0.00 41.73 4.69
6246 7504 5.977129 GCCATACAAAATAGGATTTGAACCG 59.023 40.000 6.76 0.00 41.73 4.44
6247 7505 6.872920 TGCCATACAAAATAGGATTTGAACC 58.127 36.000 6.76 0.00 41.73 3.62
6248 7506 7.010460 GCTTGCCATACAAAATAGGATTTGAAC 59.990 37.037 6.76 0.00 41.73 3.18
6249 7507 7.041107 GCTTGCCATACAAAATAGGATTTGAA 58.959 34.615 6.76 0.00 41.73 2.69
6250 7508 6.154192 TGCTTGCCATACAAAATAGGATTTGA 59.846 34.615 6.76 0.00 41.73 2.69
6251 7509 6.339730 TGCTTGCCATACAAAATAGGATTTG 58.660 36.000 0.00 0.00 44.11 2.32
6252 7510 6.543430 TGCTTGCCATACAAAATAGGATTT 57.457 33.333 0.00 0.00 37.96 2.17
6253 7511 6.543430 TTGCTTGCCATACAAAATAGGATT 57.457 33.333 0.00 0.00 37.96 3.01
6254 7512 6.155049 AGTTTGCTTGCCATACAAAATAGGAT 59.845 34.615 0.00 0.00 37.96 3.24
6255 7513 5.480073 AGTTTGCTTGCCATACAAAATAGGA 59.520 36.000 0.00 0.00 37.96 2.94
6256 7514 5.577945 CAGTTTGCTTGCCATACAAAATAGG 59.422 40.000 0.00 0.00 37.96 2.57
6257 7515 6.389091 TCAGTTTGCTTGCCATACAAAATAG 58.611 36.000 0.00 0.00 37.96 1.73
6258 7516 6.338214 TCAGTTTGCTTGCCATACAAAATA 57.662 33.333 0.00 0.00 37.96 1.40
6259 7517 5.212532 TCAGTTTGCTTGCCATACAAAAT 57.787 34.783 0.00 0.00 37.96 1.82
6260 7518 4.662468 TCAGTTTGCTTGCCATACAAAA 57.338 36.364 0.00 0.00 37.96 2.44
6261 7519 4.340666 TCTTCAGTTTGCTTGCCATACAAA 59.659 37.500 0.00 0.00 37.96 2.83
6262 7520 3.888323 TCTTCAGTTTGCTTGCCATACAA 59.112 39.130 0.00 0.00 36.62 2.41
6263 7521 3.485394 TCTTCAGTTTGCTTGCCATACA 58.515 40.909 0.00 0.00 0.00 2.29
6264 7522 4.503741 TTCTTCAGTTTGCTTGCCATAC 57.496 40.909 0.00 0.00 0.00 2.39
6265 7523 5.726980 AATTCTTCAGTTTGCTTGCCATA 57.273 34.783 0.00 0.00 0.00 2.74
6266 7524 4.612264 AATTCTTCAGTTTGCTTGCCAT 57.388 36.364 0.00 0.00 0.00 4.40
6267 7525 4.405116 AAATTCTTCAGTTTGCTTGCCA 57.595 36.364 0.00 0.00 0.00 4.92
6268 7526 6.870439 AGATTAAATTCTTCAGTTTGCTTGCC 59.130 34.615 0.00 0.00 0.00 4.52
6269 7527 7.880059 AGATTAAATTCTTCAGTTTGCTTGC 57.120 32.000 0.00 0.00 0.00 4.01
6270 7528 9.467258 TCAAGATTAAATTCTTCAGTTTGCTTG 57.533 29.630 0.00 0.00 33.69 4.01
6271 7529 9.688592 CTCAAGATTAAATTCTTCAGTTTGCTT 57.311 29.630 0.00 0.00 33.69 3.91
6272 7530 9.071276 TCTCAAGATTAAATTCTTCAGTTTGCT 57.929 29.630 0.00 0.00 33.69 3.91
6273 7531 9.339492 CTCTCAAGATTAAATTCTTCAGTTTGC 57.661 33.333 0.00 0.00 33.69 3.68
6274 7532 9.837525 CCTCTCAAGATTAAATTCTTCAGTTTG 57.162 33.333 0.00 0.00 33.69 2.93
6275 7533 9.799106 TCCTCTCAAGATTAAATTCTTCAGTTT 57.201 29.630 0.00 0.00 33.69 2.66
6276 7534 9.447157 CTCCTCTCAAGATTAAATTCTTCAGTT 57.553 33.333 0.00 0.00 33.69 3.16
6277 7535 7.552330 GCTCCTCTCAAGATTAAATTCTTCAGT 59.448 37.037 0.00 0.00 33.69 3.41
6278 7536 7.012232 GGCTCCTCTCAAGATTAAATTCTTCAG 59.988 40.741 0.00 0.00 33.69 3.02
6279 7537 6.825721 GGCTCCTCTCAAGATTAAATTCTTCA 59.174 38.462 0.00 0.00 33.69 3.02
6280 7538 6.262049 GGGCTCCTCTCAAGATTAAATTCTTC 59.738 42.308 0.00 0.00 33.69 2.87
6281 7539 6.125719 GGGCTCCTCTCAAGATTAAATTCTT 58.874 40.000 0.00 0.00 36.38 2.52
6282 7540 5.192522 TGGGCTCCTCTCAAGATTAAATTCT 59.807 40.000 0.00 0.00 0.00 2.40
6283 7541 5.440610 TGGGCTCCTCTCAAGATTAAATTC 58.559 41.667 0.00 0.00 0.00 2.17
6284 7542 5.456921 TGGGCTCCTCTCAAGATTAAATT 57.543 39.130 0.00 0.00 0.00 1.82
6285 7543 5.456921 TTGGGCTCCTCTCAAGATTAAAT 57.543 39.130 0.00 0.00 0.00 1.40
6286 7544 4.927267 TTGGGCTCCTCTCAAGATTAAA 57.073 40.909 0.00 0.00 0.00 1.52
6287 7545 4.848357 CTTTGGGCTCCTCTCAAGATTAA 58.152 43.478 0.00 0.00 0.00 1.40
6288 7546 3.370953 GCTTTGGGCTCCTCTCAAGATTA 60.371 47.826 0.00 0.00 38.06 1.75
6289 7547 2.620108 GCTTTGGGCTCCTCTCAAGATT 60.620 50.000 0.00 0.00 38.06 2.40
6290 7548 1.064832 GCTTTGGGCTCCTCTCAAGAT 60.065 52.381 0.00 0.00 38.06 2.40
6291 7549 0.326264 GCTTTGGGCTCCTCTCAAGA 59.674 55.000 0.00 0.00 38.06 3.02
6292 7550 0.679321 GGCTTTGGGCTCCTCTCAAG 60.679 60.000 0.00 0.00 41.46 3.02
6293 7551 1.136329 AGGCTTTGGGCTCCTCTCAA 61.136 55.000 0.00 0.00 45.63 3.02
6294 7552 1.539869 AGGCTTTGGGCTCCTCTCA 60.540 57.895 0.00 0.00 45.63 3.27
6295 7553 3.409384 AGGCTTTGGGCTCCTCTC 58.591 61.111 0.00 0.00 45.63 3.20
6302 7560 0.033920 CAGTTTGGAAGGCTTTGGGC 59.966 55.000 0.00 0.00 40.90 5.36
6303 7561 1.069049 CACAGTTTGGAAGGCTTTGGG 59.931 52.381 0.00 0.00 0.00 4.12
6304 7562 1.756538 ACACAGTTTGGAAGGCTTTGG 59.243 47.619 0.00 0.00 0.00 3.28
6305 7563 2.813061 CACACAGTTTGGAAGGCTTTG 58.187 47.619 0.00 0.00 0.00 2.77
6306 7564 1.136891 GCACACAGTTTGGAAGGCTTT 59.863 47.619 0.00 0.00 0.00 3.51
6307 7565 0.746659 GCACACAGTTTGGAAGGCTT 59.253 50.000 0.00 0.00 0.00 4.35
6308 7566 0.106519 AGCACACAGTTTGGAAGGCT 60.107 50.000 0.00 0.00 0.00 4.58
6309 7567 0.312102 GAGCACACAGTTTGGAAGGC 59.688 55.000 0.00 0.00 0.00 4.35
6310 7568 0.954452 GGAGCACACAGTTTGGAAGG 59.046 55.000 0.00 0.00 0.00 3.46
6311 7569 1.679139 TGGAGCACACAGTTTGGAAG 58.321 50.000 0.00 0.00 0.00 3.46
6312 7570 1.955778 CATGGAGCACACAGTTTGGAA 59.044 47.619 0.00 0.00 0.00 3.53
6313 7571 1.142667 TCATGGAGCACACAGTTTGGA 59.857 47.619 0.00 0.00 0.00 3.53
6314 7572 1.538512 CTCATGGAGCACACAGTTTGG 59.461 52.381 0.00 0.00 0.00 3.28
6315 7573 1.538512 CCTCATGGAGCACACAGTTTG 59.461 52.381 0.00 0.00 34.57 2.93
6316 7574 1.546323 CCCTCATGGAGCACACAGTTT 60.546 52.381 0.00 0.00 35.39 2.66
6317 7575 0.037303 CCCTCATGGAGCACACAGTT 59.963 55.000 0.00 0.00 35.39 3.16
6318 7576 0.837691 TCCCTCATGGAGCACACAGT 60.838 55.000 0.00 0.00 38.61 3.55
6319 7577 0.325933 TTCCCTCATGGAGCACACAG 59.674 55.000 0.00 0.00 46.24 3.66
6320 7578 0.036732 GTTCCCTCATGGAGCACACA 59.963 55.000 0.00 0.00 46.24 3.72
6321 7579 2.859992 GTTCCCTCATGGAGCACAC 58.140 57.895 0.00 0.00 46.24 3.82
6325 7583 1.753073 CCATTTGTTCCCTCATGGAGC 59.247 52.381 0.00 0.00 46.24 4.70
6326 7584 3.285484 CTCCATTTGTTCCCTCATGGAG 58.715 50.000 11.65 11.65 46.24 3.86
6327 7585 2.621407 GCTCCATTTGTTCCCTCATGGA 60.621 50.000 0.00 0.00 43.18 3.41
6328 7586 1.753073 GCTCCATTTGTTCCCTCATGG 59.247 52.381 0.00 0.00 0.00 3.66
6329 7587 2.731572 AGCTCCATTTGTTCCCTCATG 58.268 47.619 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.