Multiple sequence alignment - TraesCS2A01G330400

Loading Multiple Alignment...

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 TraesCS2A01G330400 chr2A 100.000 1504 0 0 1 1504 562685187 562686690 0.000000e+00 2778.0
1 TraesCS2A01G330400 chr2A 100.000 1135 0 0 1935 3069 562687121 562688255 0.000000e+00 2097.0
2 TraesCS2A01G330400 chr2A 95.345 623 23 3 1 618 702854344 702853723 0.000000e+00 985.0
3 TraesCS2A01G330400 chr2A 82.432 444 52 17 194 628 100200743 100200317 6.250000e-97 364.0
4 TraesCS2A01G330400 chr2D 91.667 780 29 9 753 1504 425493615 425492844 0.000000e+00 1048.0
5 TraesCS2A01G330400 chr2D 77.599 683 106 31 2243 2887 230509037 230509710 1.340000e-98 370.0
6 TraesCS2A01G330400 chr2D 89.121 239 20 3 1935 2167 425492686 425492448 2.990000e-75 292.0
7 TraesCS2A01G330400 chr2D 97.260 73 2 0 625 697 425493690 425493618 1.160000e-24 124.0
8 TraesCS2A01G330400 chr2D 91.935 62 5 0 2939 3000 425481678 425481617 1.520000e-13 87.9
9 TraesCS2A01G330400 chr3A 95.008 621 26 5 1 618 26584285 26584903 0.000000e+00 970.0
10 TraesCS2A01G330400 chr4A 95.238 588 24 4 1 586 45372842 45372257 0.000000e+00 928.0
11 TraesCS2A01G330400 chr2B 87.150 786 38 19 753 1504 500837469 500836713 0.000000e+00 833.0
12 TraesCS2A01G330400 chr2B 81.132 901 112 25 1935 2790 500836555 500835668 0.000000e+00 669.0
13 TraesCS2A01G330400 chr2B 93.421 76 2 1 625 697 500837547 500837472 3.240000e-20 110.0
14 TraesCS2A01G330400 chr2B 94.118 34 2 0 717 750 25114384 25114417 6.000000e-03 52.8
15 TraesCS2A01G330400 chr1B 86.623 456 45 8 1 454 684338049 684337608 9.890000e-135 490.0
16 TraesCS2A01G330400 chr3B 81.240 645 85 26 2181 2798 445146549 445145914 3.560000e-134 488.0
17 TraesCS2A01G330400 chr3B 79.310 580 94 17 2240 2799 669764075 669763502 1.730000e-102 383.0
18 TraesCS2A01G330400 chr3B 79.102 579 97 15 2240 2799 99674089 99673516 8.030000e-101 377.0
19 TraesCS2A01G330400 chr3D 80.944 572 79 20 2240 2792 156894648 156895208 2.830000e-115 425.0
20 TraesCS2A01G330400 chr3D 78.211 615 98 28 2208 2799 502014532 502013931 8.090000e-96 361.0
21 TraesCS2A01G330400 chr4D 78.593 668 98 23 2243 2872 484921640 484920980 1.710000e-107 399.0
22 TraesCS2A01G330400 chr4D 79.924 528 75 20 2241 2748 464849533 464850049 2.910000e-95 359.0
23 TraesCS2A01G330400 chr6B 79.483 580 93 16 2240 2799 131733627 131733054 3.710000e-104 388.0
24 TraesCS2A01G330400 chr7D 76.301 730 118 30 2208 2892 227713179 227713898 3.790000e-89 339.0
25 TraesCS2A01G330400 chrUn 76.054 735 125 27 2207 2898 9920804 9920078 4.900000e-88 335.0
26 TraesCS2A01G330400 chrUn 95.161 124 5 1 496 618 290585734 290585611 8.680000e-46 195.0
27 TraesCS2A01G330400 chr7B 82.171 129 14 6 504 631 648494365 648494245 5.410000e-18 102.0
28 TraesCS2A01G330400 chr7B 82.171 129 14 6 504 631 648547114 648546994 5.410000e-18 102.0
29 TraesCS2A01G330400 chr7B 82.171 129 14 6 504 631 648584961 648584841 5.410000e-18 102.0
30 TraesCS2A01G330400 chr5D 94.737 57 3 0 562 618 118873743 118873799 4.210000e-14 89.8
31 TraesCS2A01G330400 chr1D 89.552 67 3 4 567 631 462388094 462388030 7.050000e-12 82.4
32 TraesCS2A01G330400 chr1D 100.000 28 0 0 703 730 51571109 51571136 6.000000e-03 52.8
33 TraesCS2A01G330400 chr5B 97.059 34 1 0 717 750 612683855 612683888 1.190000e-04 58.4


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 TraesCS2A01G330400 chr2A 562685187 562688255 3068 False 2437.500000 2778 100.000000 1 3069 2 chr2A.!!$F1 3068
1 TraesCS2A01G330400 chr2A 702853723 702854344 621 True 985.000000 985 95.345000 1 618 1 chr2A.!!$R2 617
2 TraesCS2A01G330400 chr2D 425492448 425493690 1242 True 488.000000 1048 92.682667 625 2167 3 chr2D.!!$R2 1542
3 TraesCS2A01G330400 chr2D 230509037 230509710 673 False 370.000000 370 77.599000 2243 2887 1 chr2D.!!$F1 644
4 TraesCS2A01G330400 chr3A 26584285 26584903 618 False 970.000000 970 95.008000 1 618 1 chr3A.!!$F1 617
5 TraesCS2A01G330400 chr4A 45372257 45372842 585 True 928.000000 928 95.238000 1 586 1 chr4A.!!$R1 585
6 TraesCS2A01G330400 chr2B 500835668 500837547 1879 True 537.333333 833 87.234333 625 2790 3 chr2B.!!$R1 2165
7 TraesCS2A01G330400 chr3B 445145914 445146549 635 True 488.000000 488 81.240000 2181 2798 1 chr3B.!!$R2 617
8 TraesCS2A01G330400 chr3B 669763502 669764075 573 True 383.000000 383 79.310000 2240 2799 1 chr3B.!!$R3 559
9 TraesCS2A01G330400 chr3B 99673516 99674089 573 True 377.000000 377 79.102000 2240 2799 1 chr3B.!!$R1 559
10 TraesCS2A01G330400 chr3D 156894648 156895208 560 False 425.000000 425 80.944000 2240 2792 1 chr3D.!!$F1 552
11 TraesCS2A01G330400 chr3D 502013931 502014532 601 True 361.000000 361 78.211000 2208 2799 1 chr3D.!!$R1 591
12 TraesCS2A01G330400 chr4D 484920980 484921640 660 True 399.000000 399 78.593000 2243 2872 1 chr4D.!!$R1 629
13 TraesCS2A01G330400 chr4D 464849533 464850049 516 False 359.000000 359 79.924000 2241 2748 1 chr4D.!!$F1 507
14 TraesCS2A01G330400 chr6B 131733054 131733627 573 True 388.000000 388 79.483000 2240 2799 1 chr6B.!!$R1 559
15 TraesCS2A01G330400 chr7D 227713179 227713898 719 False 339.000000 339 76.301000 2208 2892 1 chr7D.!!$F1 684
16 TraesCS2A01G330400 chrUn 9920078 9920804 726 True 335.000000 335 76.054000 2207 2898 1 chrUn.!!$R1 691

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
893 907 0.878523 TCTTTTGACACCGTCCTGCG 60.879 55.0 0.0 0.0 40.95 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2801 2913 0.468226 TACGGGCATTTCAGGGCTAG 59.532 55.0 0.0 0.0 0.0 3.42 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
432 433 2.673775 TTGGAAAGGACATCAAGCCA 57.326 45.000 0.00 0.00 0.00 4.75
492 495 1.002868 CTCTGCCCAGTGGACAAGG 60.003 63.158 11.95 0.00 0.00 3.61
618 625 4.867047 CAGTCGACTGAGAATTAGCACAAT 59.133 41.667 36.73 0.00 46.59 2.71
619 626 5.349817 CAGTCGACTGAGAATTAGCACAATT 59.650 40.000 36.73 0.00 46.59 2.32
620 627 5.349817 AGTCGACTGAGAATTAGCACAATTG 59.650 40.000 19.30 3.24 0.00 2.32
621 628 5.120830 GTCGACTGAGAATTAGCACAATTGT 59.879 40.000 8.70 4.92 0.00 2.71
622 629 5.700832 TCGACTGAGAATTAGCACAATTGTT 59.299 36.000 8.77 0.00 0.00 2.83
623 630 6.204688 TCGACTGAGAATTAGCACAATTGTTT 59.795 34.615 8.77 0.00 0.00 2.83
697 707 5.991328 ATGTATGCACTGCTTGTATGTAC 57.009 39.130 1.98 0.00 32.04 2.90
699 709 6.215495 TGTATGCACTGCTTGTATGTACTA 57.785 37.500 1.98 0.00 32.04 1.82
701 711 7.272244 TGTATGCACTGCTTGTATGTACTATT 58.728 34.615 1.98 0.00 32.04 1.73
703 713 5.487433 TGCACTGCTTGTATGTACTATTGT 58.513 37.500 1.98 0.00 0.00 2.71
706 716 7.768582 TGCACTGCTTGTATGTACTATTGTATT 59.231 33.333 1.98 0.00 0.00 1.89
707 717 8.612619 GCACTGCTTGTATGTACTATTGTATTT 58.387 33.333 0.00 0.00 0.00 1.40
709 719 9.326413 ACTGCTTGTATGTACTATTGTATTTCC 57.674 33.333 0.00 0.00 0.00 3.13
710 720 9.547753 CTGCTTGTATGTACTATTGTATTTCCT 57.452 33.333 0.00 0.00 0.00 3.36
711 721 9.899661 TGCTTGTATGTACTATTGTATTTCCTT 57.100 29.630 0.00 0.00 0.00 3.36
717 727 8.833231 ATGTACTATTGTATTTCCTTCATCCG 57.167 34.615 0.00 0.00 0.00 4.18
718 728 8.014070 TGTACTATTGTATTTCCTTCATCCGA 57.986 34.615 0.00 0.00 0.00 4.55
719 729 8.479689 TGTACTATTGTATTTCCTTCATCCGAA 58.520 33.333 0.00 0.00 0.00 4.30
720 730 9.321562 GTACTATTGTATTTCCTTCATCCGAAA 57.678 33.333 0.00 0.00 32.82 3.46
721 731 8.801882 ACTATTGTATTTCCTTCATCCGAAAA 57.198 30.769 0.00 0.00 32.08 2.29
722 732 9.408648 ACTATTGTATTTCCTTCATCCGAAAAT 57.591 29.630 0.00 0.00 32.08 1.82
725 735 8.801882 TTGTATTTCCTTCATCCGAAAATACT 57.198 30.769 14.03 0.00 35.37 2.12
726 736 8.801882 TGTATTTCCTTCATCCGAAAATACTT 57.198 30.769 14.03 0.00 35.37 2.24
727 737 8.673711 TGTATTTCCTTCATCCGAAAATACTTG 58.326 33.333 14.03 0.00 35.37 3.16
728 738 7.703058 ATTTCCTTCATCCGAAAATACTTGT 57.297 32.000 0.00 0.00 32.08 3.16
729 739 6.737254 TTCCTTCATCCGAAAATACTTGTC 57.263 37.500 0.00 0.00 0.00 3.18
730 740 4.868171 TCCTTCATCCGAAAATACTTGTCG 59.132 41.667 0.00 0.00 34.58 4.35
731 741 4.630069 CCTTCATCCGAAAATACTTGTCGT 59.370 41.667 0.00 0.00 32.93 4.34
732 742 5.808540 CCTTCATCCGAAAATACTTGTCGTA 59.191 40.000 0.00 0.00 32.93 3.43
733 743 6.019801 CCTTCATCCGAAAATACTTGTCGTAG 60.020 42.308 0.00 0.00 32.93 3.51
734 744 6.198650 TCATCCGAAAATACTTGTCGTAGA 57.801 37.500 0.00 0.00 32.93 2.59
735 745 6.263344 TCATCCGAAAATACTTGTCGTAGAG 58.737 40.000 0.00 0.00 36.95 2.43
736 746 5.885230 TCCGAAAATACTTGTCGTAGAGA 57.115 39.130 0.00 0.00 36.95 3.10
737 747 6.446781 TCCGAAAATACTTGTCGTAGAGAT 57.553 37.500 0.00 0.00 36.95 2.75
738 748 6.263344 TCCGAAAATACTTGTCGTAGAGATG 58.737 40.000 0.00 0.00 36.95 2.90
739 749 5.459107 CCGAAAATACTTGTCGTAGAGATGG 59.541 44.000 0.00 0.00 36.95 3.51
740 750 6.263344 CGAAAATACTTGTCGTAGAGATGGA 58.737 40.000 0.00 0.00 36.95 3.41
741 751 6.918569 CGAAAATACTTGTCGTAGAGATGGAT 59.081 38.462 0.00 0.00 36.95 3.41
742 752 7.096436 CGAAAATACTTGTCGTAGAGATGGATG 60.096 40.741 0.00 0.00 36.95 3.51
743 753 6.716934 AATACTTGTCGTAGAGATGGATGT 57.283 37.500 0.00 0.00 36.95 3.06
744 754 7.818997 AATACTTGTCGTAGAGATGGATGTA 57.181 36.000 0.00 0.00 36.95 2.29
745 755 8.410673 AATACTTGTCGTAGAGATGGATGTAT 57.589 34.615 0.00 0.00 36.95 2.29
746 756 6.320494 ACTTGTCGTAGAGATGGATGTATC 57.680 41.667 0.00 0.00 36.95 2.24
747 757 6.065374 ACTTGTCGTAGAGATGGATGTATCT 58.935 40.000 0.00 0.00 40.02 1.98
748 758 7.225011 ACTTGTCGTAGAGATGGATGTATCTA 58.775 38.462 0.00 0.00 37.53 1.98
749 759 7.389330 ACTTGTCGTAGAGATGGATGTATCTAG 59.611 40.741 0.00 0.00 37.53 2.43
750 760 6.174049 TGTCGTAGAGATGGATGTATCTAGG 58.826 44.000 0.00 0.00 37.53 3.02
751 761 6.013639 TGTCGTAGAGATGGATGTATCTAGGA 60.014 42.308 0.00 0.00 37.53 2.94
752 762 6.537301 GTCGTAGAGATGGATGTATCTAGGAG 59.463 46.154 4.28 0.00 38.88 3.69
753 763 6.213802 TCGTAGAGATGGATGTATCTAGGAGT 59.786 42.308 0.00 0.00 37.53 3.85
754 764 7.399478 TCGTAGAGATGGATGTATCTAGGAGTA 59.601 40.741 0.00 0.00 37.53 2.59
755 765 7.709182 CGTAGAGATGGATGTATCTAGGAGTAG 59.291 44.444 0.00 0.00 37.53 2.57
756 766 7.822749 AGAGATGGATGTATCTAGGAGTAGA 57.177 40.000 0.00 0.00 37.53 2.59
757 767 8.225863 AGAGATGGATGTATCTAGGAGTAGAA 57.774 38.462 0.00 0.00 38.82 2.10
758 768 8.845793 AGAGATGGATGTATCTAGGAGTAGAAT 58.154 37.037 0.00 0.00 38.82 2.40
759 769 9.474313 GAGATGGATGTATCTAGGAGTAGAATT 57.526 37.037 0.00 0.00 38.82 2.17
795 808 5.482908 TGAGAGATTGAGAGCCAACTTTAC 58.517 41.667 0.00 0.00 37.63 2.01
801 814 1.813178 GAGAGCCAACTTTACTTGGGC 59.187 52.381 0.00 0.00 41.12 5.36
855 868 3.505386 TCTGAAGAACAAGAGCTCTCCT 58.495 45.455 18.55 9.22 0.00 3.69
859 873 2.733956 AGAACAAGAGCTCTCCTCGAT 58.266 47.619 18.55 0.00 45.54 3.59
893 907 0.878523 TCTTTTGACACCGTCCTGCG 60.879 55.000 0.00 0.00 40.95 5.18
1006 1030 1.568612 CGGCAGTTGCACGATGAAGT 61.569 55.000 6.43 0.00 44.36 3.01
1008 1032 1.664016 GGCAGTTGCACGATGAAGTTG 60.664 52.381 6.43 0.00 44.36 3.16
1018 1042 0.387239 GATGAAGTTGGTGGTTGCGC 60.387 55.000 0.00 0.00 0.00 6.09
1104 1149 1.667154 CCGAGATCCTGACGCCAGAA 61.667 60.000 0.00 0.00 43.02 3.02
1123 1168 2.677848 GGCCCTTCCAGACCTTCC 59.322 66.667 0.00 0.00 34.01 3.46
1252 1297 1.272212 TCCACCCGTCGGTAACTTAAC 59.728 52.381 11.06 0.00 42.04 2.01
1263 1308 6.294363 GTCGGTAACTTAACTTTTCATCACG 58.706 40.000 0.00 0.00 0.00 4.35
1301 1346 3.753797 CCATCGTCTCGATCTGATAGGAA 59.246 47.826 1.58 0.00 45.19 3.36
1302 1347 4.397730 CCATCGTCTCGATCTGATAGGAAT 59.602 45.833 1.58 0.00 45.19 3.01
1303 1348 5.586643 CCATCGTCTCGATCTGATAGGAATA 59.413 44.000 1.58 0.00 45.19 1.75
1304 1349 6.238347 CCATCGTCTCGATCTGATAGGAATAG 60.238 46.154 1.58 0.00 45.19 1.73
1305 1350 5.179533 TCGTCTCGATCTGATAGGAATAGG 58.820 45.833 0.00 0.00 0.00 2.57
1306 1351 5.046520 TCGTCTCGATCTGATAGGAATAGGA 60.047 44.000 0.00 0.00 0.00 2.94
1474 1522 2.866460 GCTGTACATGGTGAACGTGACT 60.866 50.000 0.00 0.00 39.46 3.41
1476 1524 3.127589 TGTACATGGTGAACGTGACTTG 58.872 45.455 0.00 0.00 39.46 3.16
1974 2022 2.936032 GACCCCTGGAGGCAAGGT 60.936 66.667 0.00 0.00 32.45 3.50
1978 2026 2.538141 CCCTGGAGGCAAGGTGGAA 61.538 63.158 0.00 0.00 32.45 3.53
1984 2032 0.112412 GAGGCAAGGTGGAAGGGAAA 59.888 55.000 0.00 0.00 0.00 3.13
1987 2035 1.704641 GCAAGGTGGAAGGGAAAAGT 58.295 50.000 0.00 0.00 0.00 2.66
2117 2168 3.937706 GTGCAGTGAATTGCTCTACTGAT 59.062 43.478 7.35 0.00 44.38 2.90
2118 2169 4.033817 GTGCAGTGAATTGCTCTACTGATC 59.966 45.833 7.35 0.00 44.38 2.92
2127 2178 5.697473 TTGCTCTACTGATCGAGATTAGG 57.303 43.478 9.24 0.00 0.00 2.69
2132 2186 7.045416 GCTCTACTGATCGAGATTAGGATAGA 58.955 42.308 9.24 7.19 0.00 1.98
2139 2193 7.644062 TGATCGAGATTAGGATAGATTAGGGT 58.356 38.462 0.00 0.00 0.00 4.34
2142 2196 6.885376 TCGAGATTAGGATAGATTAGGGTGAC 59.115 42.308 0.00 0.00 0.00 3.67
2145 2199 7.239438 AGATTAGGATAGATTAGGGTGACGAA 58.761 38.462 0.00 0.00 0.00 3.85
2158 2212 5.183228 AGGGTGACGAATTAAACGATGATT 58.817 37.500 11.31 0.00 34.70 2.57
2185 2255 1.923204 CGACGGCTGATTTTCTCTCAG 59.077 52.381 0.00 0.00 42.47 3.35
2192 2262 4.759183 GGCTGATTTTCTCTCAGAAACAGT 59.241 41.667 13.79 0.52 43.25 3.55
2196 2266 7.386299 GCTGATTTTCTCTCAGAAACAGTCTTA 59.614 37.037 13.79 0.00 43.25 2.10
2205 2275 3.600898 AACAGTCTTACGCCCCGCC 62.601 63.158 0.00 0.00 0.00 6.13
2273 2349 2.046313 CAGCACAATCACGCTCAAAAC 58.954 47.619 0.00 0.00 35.96 2.43
2281 2358 3.585748 TCACGCTCAAAACGAAAAGAG 57.414 42.857 0.00 0.00 0.00 2.85
2420 2512 3.436243 ACCAAACAACACCTCCAAGAAA 58.564 40.909 0.00 0.00 0.00 2.52
2423 2515 2.364972 ACAACACCTCCAAGAAAGGG 57.635 50.000 0.00 0.00 38.29 3.95
2502 2597 2.202623 GTAGCACCCGACGCTCTG 60.203 66.667 0.00 0.00 40.96 3.35
2528 2623 3.062466 CTCGACGGCACCCTCAGA 61.062 66.667 0.00 0.00 0.00 3.27
2551 2646 4.657824 CCGCGTTGGTGTCGGACT 62.658 66.667 4.92 0.00 45.53 3.85
2554 2649 2.420043 CGTTGGTGTCGGACTGGT 59.580 61.111 9.88 0.00 0.00 4.00
2562 2657 2.114625 TCGGACTGGTCGACTGGT 59.885 61.111 16.46 14.00 0.00 4.00
2618 2714 0.103208 GAGCACTCCACCATACCGAG 59.897 60.000 0.00 0.00 0.00 4.63
2632 2741 1.079819 CCGAGCACCACGATCTTGT 60.080 57.895 0.00 0.00 0.00 3.16
2664 2773 1.961277 GTCTCACCACGGCACCAAG 60.961 63.158 0.00 0.00 0.00 3.61
2793 2905 1.885887 GCAACAACAGGAGCATACCAA 59.114 47.619 0.00 0.00 0.00 3.67
2799 2911 2.203209 GGAGCATACCAAGCCCGG 60.203 66.667 0.00 0.00 0.00 5.73
2800 2912 2.902343 GAGCATACCAAGCCCGGC 60.902 66.667 0.00 0.00 0.00 6.13
2801 2913 4.506255 AGCATACCAAGCCCGGCC 62.506 66.667 5.55 0.00 0.00 6.13
2802 2914 4.506255 GCATACCAAGCCCGGCCT 62.506 66.667 5.55 0.00 0.00 5.19
2823 2951 0.892063 GCCCTGAAATGCCCGTAAAA 59.108 50.000 0.00 0.00 0.00 1.52
2831 2959 3.493440 GCCCGTAAAACTCCCGCG 61.493 66.667 0.00 0.00 0.00 6.46
2832 2960 2.816520 CCCGTAAAACTCCCGCGG 60.817 66.667 21.04 21.04 41.82 6.46
2893 3021 3.847602 CGAGCTGCCCCTCCTCTG 61.848 72.222 0.00 0.00 0.00 3.35
2910 3038 4.152625 GCACCGCGCAGTAAGCAG 62.153 66.667 8.75 0.00 46.13 4.24
2911 3039 4.152625 CACCGCGCAGTAAGCAGC 62.153 66.667 8.75 0.00 46.13 5.25
2917 3045 3.198489 GCAGTAAGCAGCGAGGCC 61.198 66.667 0.00 0.00 44.79 5.19
2918 3046 2.581354 CAGTAAGCAGCGAGGCCT 59.419 61.111 3.86 3.86 0.00 5.19
2919 3047 1.520342 CAGTAAGCAGCGAGGCCTC 60.520 63.158 23.79 23.79 0.00 4.70
2920 3048 1.984570 AGTAAGCAGCGAGGCCTCA 60.985 57.895 31.67 8.16 0.00 3.86
2921 3049 1.811679 GTAAGCAGCGAGGCCTCAC 60.812 63.158 31.67 23.10 0.00 3.51
2922 3050 1.984570 TAAGCAGCGAGGCCTCACT 60.985 57.895 31.67 25.12 0.00 3.41
2923 3051 2.230994 TAAGCAGCGAGGCCTCACTG 62.231 60.000 36.28 36.28 41.36 3.66
2925 3053 3.385384 CAGCGAGGCCTCACTGGA 61.385 66.667 34.13 0.00 36.43 3.86
2926 3054 3.073735 AGCGAGGCCTCACTGGAG 61.074 66.667 31.67 15.56 41.02 3.86
2927 3055 4.828925 GCGAGGCCTCACTGGAGC 62.829 72.222 31.67 21.29 39.96 4.70
2928 3056 3.073735 CGAGGCCTCACTGGAGCT 61.074 66.667 31.67 0.00 39.96 4.09
2929 3057 1.754621 CGAGGCCTCACTGGAGCTA 60.755 63.158 31.67 0.00 39.96 3.32
2930 3058 1.733402 CGAGGCCTCACTGGAGCTAG 61.733 65.000 31.67 8.04 39.96 3.42
2931 3059 2.026945 GAGGCCTCACTGGAGCTAGC 62.027 65.000 28.43 6.62 39.96 3.42
2932 3060 2.503546 GCCTCACTGGAGCTAGCC 59.496 66.667 12.13 2.59 39.96 3.93
2933 3061 3.100503 GCCTCACTGGAGCTAGCCC 62.101 68.421 12.13 13.02 39.96 5.19
2934 3062 1.687146 CCTCACTGGAGCTAGCCCA 60.687 63.158 19.82 19.82 39.96 5.36
2935 3063 1.519719 CTCACTGGAGCTAGCCCAC 59.480 63.158 17.87 7.29 33.67 4.61
2936 3064 1.965754 CTCACTGGAGCTAGCCCACC 61.966 65.000 17.87 15.85 33.67 4.61
2937 3065 2.689034 ACTGGAGCTAGCCCACCC 60.689 66.667 17.87 12.04 0.00 4.61
2938 3066 3.854669 CTGGAGCTAGCCCACCCG 61.855 72.222 17.87 9.67 0.00 5.28
2949 3077 4.939368 CCACCCGGCCGACAACAA 62.939 66.667 30.73 0.00 0.00 2.83
2950 3078 2.902846 CACCCGGCCGACAACAAA 60.903 61.111 30.73 0.00 0.00 2.83
2951 3079 2.903350 ACCCGGCCGACAACAAAC 60.903 61.111 30.73 0.00 0.00 2.93
2952 3080 3.666253 CCCGGCCGACAACAAACC 61.666 66.667 30.73 0.00 0.00 3.27
2953 3081 2.593436 CCGGCCGACAACAAACCT 60.593 61.111 30.73 0.00 0.00 3.50
2954 3082 2.613506 CCGGCCGACAACAAACCTC 61.614 63.158 30.73 0.00 0.00 3.85
2955 3083 1.890041 CGGCCGACAACAAACCTCA 60.890 57.895 24.07 0.00 0.00 3.86
2956 3084 1.440938 CGGCCGACAACAAACCTCAA 61.441 55.000 24.07 0.00 0.00 3.02
2957 3085 0.310854 GGCCGACAACAAACCTCAAG 59.689 55.000 0.00 0.00 0.00 3.02
2958 3086 1.305201 GCCGACAACAAACCTCAAGA 58.695 50.000 0.00 0.00 0.00 3.02
2959 3087 1.880027 GCCGACAACAAACCTCAAGAT 59.120 47.619 0.00 0.00 0.00 2.40
2960 3088 2.095718 GCCGACAACAAACCTCAAGATC 60.096 50.000 0.00 0.00 0.00 2.75
2961 3089 3.403038 CCGACAACAAACCTCAAGATCT 58.597 45.455 0.00 0.00 0.00 2.75
2962 3090 4.566004 CCGACAACAAACCTCAAGATCTA 58.434 43.478 0.00 0.00 0.00 1.98
2963 3091 4.627467 CCGACAACAAACCTCAAGATCTAG 59.373 45.833 0.00 0.00 0.00 2.43
2964 3092 5.470368 CGACAACAAACCTCAAGATCTAGA 58.530 41.667 0.00 0.00 0.00 2.43
2965 3093 5.926542 CGACAACAAACCTCAAGATCTAGAA 59.073 40.000 0.00 0.00 0.00 2.10
2966 3094 6.128795 CGACAACAAACCTCAAGATCTAGAAC 60.129 42.308 0.00 0.00 0.00 3.01
2967 3095 5.998363 ACAACAAACCTCAAGATCTAGAACC 59.002 40.000 0.00 0.00 0.00 3.62
2968 3096 4.822026 ACAAACCTCAAGATCTAGAACCG 58.178 43.478 0.00 0.00 0.00 4.44
2969 3097 4.527038 ACAAACCTCAAGATCTAGAACCGA 59.473 41.667 0.00 0.00 0.00 4.69
2970 3098 4.722361 AACCTCAAGATCTAGAACCGAC 57.278 45.455 0.00 0.00 0.00 4.79
2971 3099 2.683867 ACCTCAAGATCTAGAACCGACG 59.316 50.000 0.00 0.00 0.00 5.12
2972 3100 2.943690 CCTCAAGATCTAGAACCGACGA 59.056 50.000 0.00 0.00 0.00 4.20
2973 3101 3.377485 CCTCAAGATCTAGAACCGACGAA 59.623 47.826 0.00 0.00 0.00 3.85
2974 3102 4.344448 CTCAAGATCTAGAACCGACGAAC 58.656 47.826 0.00 0.00 0.00 3.95
2975 3103 4.008330 TCAAGATCTAGAACCGACGAACT 58.992 43.478 0.00 0.00 0.00 3.01
2976 3104 5.181009 TCAAGATCTAGAACCGACGAACTA 58.819 41.667 0.00 0.00 0.00 2.24
2977 3105 5.064452 TCAAGATCTAGAACCGACGAACTAC 59.936 44.000 0.00 0.00 0.00 2.73
2979 3107 2.959516 TCTAGAACCGACGAACTACGA 58.040 47.619 0.00 0.00 45.77 3.43
2980 3108 3.525537 TCTAGAACCGACGAACTACGAT 58.474 45.455 0.00 0.00 45.77 3.73
2981 3109 2.539346 AGAACCGACGAACTACGATG 57.461 50.000 0.00 0.00 45.77 3.84
2982 3110 0.912528 GAACCGACGAACTACGATGC 59.087 55.000 0.00 0.00 45.77 3.91
2983 3111 0.457337 AACCGACGAACTACGATGCC 60.457 55.000 0.00 0.00 45.77 4.40
2984 3112 1.138036 CCGACGAACTACGATGCCA 59.862 57.895 0.00 0.00 45.77 4.92
2985 3113 0.866061 CCGACGAACTACGATGCCAG 60.866 60.000 0.00 0.00 45.77 4.85
2986 3114 0.098200 CGACGAACTACGATGCCAGA 59.902 55.000 0.00 0.00 45.77 3.86
2987 3115 1.466866 CGACGAACTACGATGCCAGAA 60.467 52.381 0.00 0.00 45.77 3.02
2988 3116 2.602878 GACGAACTACGATGCCAGAAA 58.397 47.619 0.00 0.00 45.77 2.52
2989 3117 2.991190 GACGAACTACGATGCCAGAAAA 59.009 45.455 0.00 0.00 45.77 2.29
2990 3118 3.596214 ACGAACTACGATGCCAGAAAAT 58.404 40.909 0.00 0.00 45.77 1.82
2991 3119 4.751060 ACGAACTACGATGCCAGAAAATA 58.249 39.130 0.00 0.00 45.77 1.40
2992 3120 5.357257 ACGAACTACGATGCCAGAAAATAT 58.643 37.500 0.00 0.00 45.77 1.28
2993 3121 5.462398 ACGAACTACGATGCCAGAAAATATC 59.538 40.000 0.00 0.00 45.77 1.63
2994 3122 5.462068 CGAACTACGATGCCAGAAAATATCA 59.538 40.000 0.00 0.00 45.77 2.15
2995 3123 6.562270 CGAACTACGATGCCAGAAAATATCAC 60.562 42.308 0.00 0.00 45.77 3.06
2996 3124 5.670485 ACTACGATGCCAGAAAATATCACA 58.330 37.500 0.00 0.00 0.00 3.58
2997 3125 6.291377 ACTACGATGCCAGAAAATATCACAT 58.709 36.000 0.00 0.00 0.00 3.21
2998 3126 5.428496 ACGATGCCAGAAAATATCACATG 57.572 39.130 0.00 0.00 0.00 3.21
2999 3127 4.883585 ACGATGCCAGAAAATATCACATGT 59.116 37.500 0.00 0.00 0.00 3.21
3000 3128 5.357878 ACGATGCCAGAAAATATCACATGTT 59.642 36.000 0.00 0.00 0.00 2.71
3001 3129 5.684184 CGATGCCAGAAAATATCACATGTTG 59.316 40.000 0.00 0.00 0.00 3.33
3002 3130 6.458615 CGATGCCAGAAAATATCACATGTTGA 60.459 38.462 0.00 0.00 39.11 3.18
3004 3132 7.172868 TGCCAGAAAATATCACATGTTGATT 57.827 32.000 13.57 4.09 42.87 2.57
3005 3133 8.291191 TGCCAGAAAATATCACATGTTGATTA 57.709 30.769 13.57 0.00 42.87 1.75
3006 3134 8.190122 TGCCAGAAAATATCACATGTTGATTAC 58.810 33.333 13.57 5.28 42.87 1.89
3007 3135 7.376866 GCCAGAAAATATCACATGTTGATTACG 59.623 37.037 13.57 0.00 42.87 3.18
3008 3136 7.857389 CCAGAAAATATCACATGTTGATTACGG 59.143 37.037 13.57 5.75 42.87 4.02
3009 3137 8.611757 CAGAAAATATCACATGTTGATTACGGA 58.388 33.333 13.57 0.00 42.87 4.69
3010 3138 8.612619 AGAAAATATCACATGTTGATTACGGAC 58.387 33.333 13.57 5.31 42.87 4.79
3011 3139 8.506168 AAAATATCACATGTTGATTACGGACT 57.494 30.769 13.57 0.00 42.87 3.85
3012 3140 9.607988 AAAATATCACATGTTGATTACGGACTA 57.392 29.630 13.57 0.00 42.87 2.59
3013 3141 9.778741 AAATATCACATGTTGATTACGGACTAT 57.221 29.630 13.57 0.56 42.87 2.12
3014 3142 9.778741 AATATCACATGTTGATTACGGACTATT 57.221 29.630 13.57 5.18 42.87 1.73
3017 3145 9.778741 ATCACATGTTGATTACGGACTATTATT 57.221 29.630 0.00 0.00 42.87 1.40
3018 3146 9.256477 TCACATGTTGATTACGGACTATTATTC 57.744 33.333 0.00 0.00 0.00 1.75
3019 3147 9.261180 CACATGTTGATTACGGACTATTATTCT 57.739 33.333 0.00 0.00 0.00 2.40
3023 3151 9.740239 TGTTGATTACGGACTATTATTCTACAC 57.260 33.333 0.00 0.00 0.00 2.90
3024 3152 9.962783 GTTGATTACGGACTATTATTCTACACT 57.037 33.333 0.00 0.00 0.00 3.55
3025 3153 9.961265 TTGATTACGGACTATTATTCTACACTG 57.039 33.333 0.00 0.00 0.00 3.66
3026 3154 8.080417 TGATTACGGACTATTATTCTACACTGC 58.920 37.037 0.00 0.00 0.00 4.40
3027 3155 5.197682 ACGGACTATTATTCTACACTGCC 57.802 43.478 0.00 0.00 0.00 4.85
3028 3156 4.894114 ACGGACTATTATTCTACACTGCCT 59.106 41.667 0.00 0.00 0.00 4.75
3029 3157 5.363005 ACGGACTATTATTCTACACTGCCTT 59.637 40.000 0.00 0.00 0.00 4.35
3030 3158 5.692204 CGGACTATTATTCTACACTGCCTTG 59.308 44.000 0.00 0.00 0.00 3.61
3031 3159 6.583562 GGACTATTATTCTACACTGCCTTGT 58.416 40.000 0.00 0.00 0.00 3.16
3032 3160 6.702282 GGACTATTATTCTACACTGCCTTGTC 59.298 42.308 0.00 0.00 0.00 3.18
3033 3161 7.182817 ACTATTATTCTACACTGCCTTGTCA 57.817 36.000 0.00 0.00 0.00 3.58
3034 3162 7.620880 ACTATTATTCTACACTGCCTTGTCAA 58.379 34.615 0.00 0.00 0.00 3.18
3035 3163 8.100791 ACTATTATTCTACACTGCCTTGTCAAA 58.899 33.333 0.00 0.00 0.00 2.69
3036 3164 7.759489 ATTATTCTACACTGCCTTGTCAAAA 57.241 32.000 0.00 0.00 0.00 2.44
3037 3165 4.893424 TTCTACACTGCCTTGTCAAAAC 57.107 40.909 0.00 0.00 0.00 2.43
3038 3166 4.150897 TCTACACTGCCTTGTCAAAACT 57.849 40.909 0.00 0.00 0.00 2.66
3039 3167 5.284861 TCTACACTGCCTTGTCAAAACTA 57.715 39.130 0.00 0.00 0.00 2.24
3040 3168 5.054477 TCTACACTGCCTTGTCAAAACTAC 58.946 41.667 0.00 0.00 0.00 2.73
3041 3169 3.616219 ACACTGCCTTGTCAAAACTACA 58.384 40.909 0.00 0.00 0.00 2.74
3042 3170 3.377172 ACACTGCCTTGTCAAAACTACAC 59.623 43.478 0.00 0.00 0.00 2.90
3043 3171 2.949644 ACTGCCTTGTCAAAACTACACC 59.050 45.455 0.00 0.00 0.00 4.16
3044 3172 2.948979 CTGCCTTGTCAAAACTACACCA 59.051 45.455 0.00 0.00 0.00 4.17
3045 3173 3.561143 TGCCTTGTCAAAACTACACCAT 58.439 40.909 0.00 0.00 0.00 3.55
3046 3174 3.568007 TGCCTTGTCAAAACTACACCATC 59.432 43.478 0.00 0.00 0.00 3.51
3047 3175 3.568007 GCCTTGTCAAAACTACACCATCA 59.432 43.478 0.00 0.00 0.00 3.07
3048 3176 4.037446 GCCTTGTCAAAACTACACCATCAA 59.963 41.667 0.00 0.00 0.00 2.57
3049 3177 5.451242 GCCTTGTCAAAACTACACCATCAAA 60.451 40.000 0.00 0.00 0.00 2.69
3050 3178 6.568869 CCTTGTCAAAACTACACCATCAAAA 58.431 36.000 0.00 0.00 0.00 2.44
3051 3179 6.475402 CCTTGTCAAAACTACACCATCAAAAC 59.525 38.462 0.00 0.00 0.00 2.43
3052 3180 5.897050 TGTCAAAACTACACCATCAAAACC 58.103 37.500 0.00 0.00 0.00 3.27
3053 3181 5.419155 TGTCAAAACTACACCATCAAAACCA 59.581 36.000 0.00 0.00 0.00 3.67
3054 3182 6.097554 TGTCAAAACTACACCATCAAAACCAT 59.902 34.615 0.00 0.00 0.00 3.55
3055 3183 7.285629 TGTCAAAACTACACCATCAAAACCATA 59.714 33.333 0.00 0.00 0.00 2.74
3056 3184 7.593644 GTCAAAACTACACCATCAAAACCATAC 59.406 37.037 0.00 0.00 0.00 2.39
3057 3185 7.285629 TCAAAACTACACCATCAAAACCATACA 59.714 33.333 0.00 0.00 0.00 2.29
3058 3186 7.589958 AAACTACACCATCAAAACCATACAA 57.410 32.000 0.00 0.00 0.00 2.41
3059 3187 7.589958 AACTACACCATCAAAACCATACAAA 57.410 32.000 0.00 0.00 0.00 2.83
3060 3188 6.977213 ACTACACCATCAAAACCATACAAAC 58.023 36.000 0.00 0.00 0.00 2.93
3061 3189 5.208463 ACACCATCAAAACCATACAAACC 57.792 39.130 0.00 0.00 0.00 3.27
3062 3190 4.898861 ACACCATCAAAACCATACAAACCT 59.101 37.500 0.00 0.00 0.00 3.50
3063 3191 6.071984 ACACCATCAAAACCATACAAACCTA 58.928 36.000 0.00 0.00 0.00 3.08
3064 3192 6.551601 ACACCATCAAAACCATACAAACCTAA 59.448 34.615 0.00 0.00 0.00 2.69
3065 3193 7.234577 ACACCATCAAAACCATACAAACCTAAT 59.765 33.333 0.00 0.00 0.00 1.73
3066 3194 8.744652 CACCATCAAAACCATACAAACCTAATA 58.255 33.333 0.00 0.00 0.00 0.98
3067 3195 9.487442 ACCATCAAAACCATACAAACCTAATAT 57.513 29.630 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 6.518493 TCAGTACTGTTAAATCTCAAACGGT 58.482 36.000 21.99 5.16 44.99 4.83
424 425 2.360350 CGTGGGCTGTGGCTTGAT 60.360 61.111 0.00 0.00 38.73 2.57
492 495 3.071479 TCTCGTCCAAAAACATACTGGC 58.929 45.455 0.00 0.00 0.00 4.85
524 527 3.008266 TGATCAGTGATTTGTGGCTGAGA 59.992 43.478 7.16 0.00 40.67 3.27
618 625 6.037098 CCATTTCGGCGGAATAAATAAACAA 58.963 36.000 14.01 0.00 30.88 2.83
619 626 5.125739 ACCATTTCGGCGGAATAAATAAACA 59.874 36.000 14.01 0.00 39.03 2.83
620 627 5.457473 CACCATTTCGGCGGAATAAATAAAC 59.543 40.000 14.01 0.00 39.03 2.01
621 628 5.125739 ACACCATTTCGGCGGAATAAATAAA 59.874 36.000 14.01 0.45 39.03 1.40
622 629 4.641094 ACACCATTTCGGCGGAATAAATAA 59.359 37.500 14.01 0.00 39.03 1.40
623 630 4.200874 ACACCATTTCGGCGGAATAAATA 58.799 39.130 14.01 0.00 39.03 1.40
663 673 5.564063 GCAGTGCATACATTATGATGTGCAT 60.564 40.000 15.72 0.61 45.80 3.96
699 709 9.408648 AGTATTTTCGGATGAAGGAAATACAAT 57.591 29.630 17.32 1.48 37.56 2.71
701 711 8.673711 CAAGTATTTTCGGATGAAGGAAATACA 58.326 33.333 17.32 0.00 37.56 2.29
703 713 8.801882 ACAAGTATTTTCGGATGAAGGAAATA 57.198 30.769 0.00 0.00 35.06 1.40
706 716 5.350365 CGACAAGTATTTTCGGATGAAGGAA 59.650 40.000 0.00 0.00 35.06 3.36
707 717 4.868171 CGACAAGTATTTTCGGATGAAGGA 59.132 41.667 0.00 0.00 35.06 3.36
708 718 4.630069 ACGACAAGTATTTTCGGATGAAGG 59.370 41.667 0.00 0.00 37.07 3.46
709 719 5.779806 ACGACAAGTATTTTCGGATGAAG 57.220 39.130 0.00 0.00 37.07 3.02
710 720 6.623486 TCTACGACAAGTATTTTCGGATGAA 58.377 36.000 0.00 0.00 37.07 2.57
711 721 6.094464 TCTCTACGACAAGTATTTTCGGATGA 59.906 38.462 0.00 0.00 37.07 2.92
712 722 6.263344 TCTCTACGACAAGTATTTTCGGATG 58.737 40.000 0.00 0.00 37.07 3.51
713 723 6.446781 TCTCTACGACAAGTATTTTCGGAT 57.553 37.500 0.00 0.00 37.07 4.18
714 724 5.885230 TCTCTACGACAAGTATTTTCGGA 57.115 39.130 0.00 0.00 37.07 4.55
715 725 5.459107 CCATCTCTACGACAAGTATTTTCGG 59.541 44.000 0.00 0.00 37.07 4.30
716 726 6.263344 TCCATCTCTACGACAAGTATTTTCG 58.737 40.000 0.00 0.00 38.73 3.46
717 727 7.707035 ACATCCATCTCTACGACAAGTATTTTC 59.293 37.037 0.00 0.00 34.34 2.29
718 728 7.556844 ACATCCATCTCTACGACAAGTATTTT 58.443 34.615 0.00 0.00 34.34 1.82
719 729 7.113658 ACATCCATCTCTACGACAAGTATTT 57.886 36.000 0.00 0.00 34.34 1.40
720 730 6.716934 ACATCCATCTCTACGACAAGTATT 57.283 37.500 0.00 0.00 34.34 1.89
721 731 7.885922 AGATACATCCATCTCTACGACAAGTAT 59.114 37.037 0.00 0.00 34.34 2.12
722 732 7.225011 AGATACATCCATCTCTACGACAAGTA 58.775 38.462 0.00 0.00 28.83 2.24
723 733 6.065374 AGATACATCCATCTCTACGACAAGT 58.935 40.000 0.00 0.00 28.83 3.16
724 734 6.567687 AGATACATCCATCTCTACGACAAG 57.432 41.667 0.00 0.00 28.83 3.16
725 735 6.655425 CCTAGATACATCCATCTCTACGACAA 59.345 42.308 0.00 0.00 36.63 3.18
726 736 6.013639 TCCTAGATACATCCATCTCTACGACA 60.014 42.308 0.00 0.00 36.63 4.35
727 737 6.408035 TCCTAGATACATCCATCTCTACGAC 58.592 44.000 0.00 0.00 36.63 4.34
728 738 6.213802 ACTCCTAGATACATCCATCTCTACGA 59.786 42.308 0.00 0.00 36.63 3.43
729 739 6.411376 ACTCCTAGATACATCCATCTCTACG 58.589 44.000 0.00 0.00 36.63 3.51
730 740 8.764558 TCTACTCCTAGATACATCCATCTCTAC 58.235 40.741 0.00 0.00 36.63 2.59
731 741 8.919018 TCTACTCCTAGATACATCCATCTCTA 57.081 38.462 0.00 0.00 36.63 2.43
732 742 7.822749 TCTACTCCTAGATACATCCATCTCT 57.177 40.000 0.00 0.00 36.63 3.10
733 743 9.474313 AATTCTACTCCTAGATACATCCATCTC 57.526 37.037 0.00 0.00 36.63 2.75
760 770 7.812191 GCTCTCAATCTCTCATGTTTACGATAT 59.188 37.037 0.00 0.00 0.00 1.63
765 775 5.423015 TGGCTCTCAATCTCTCATGTTTAC 58.577 41.667 0.00 0.00 0.00 2.01
777 787 4.156739 CCCAAGTAAAGTTGGCTCTCAATC 59.843 45.833 10.57 0.00 45.08 2.67
795 808 0.110238 CGTTGATTCACGTGCCCAAG 60.110 55.000 11.67 5.39 35.34 3.61
816 829 5.961395 TCAGAACGTAACTGAAAACAGAC 57.039 39.130 18.57 0.00 40.70 3.51
853 866 0.673437 GGAGGCAAGAGAGATCGAGG 59.327 60.000 0.00 0.00 0.00 4.63
855 868 0.394488 ACGGAGGCAAGAGAGATCGA 60.394 55.000 0.00 0.00 0.00 3.59
859 873 1.633774 AAAGACGGAGGCAAGAGAGA 58.366 50.000 0.00 0.00 0.00 3.10
893 907 0.745468 AGGCGGTTAAGAGGATCGAC 59.255 55.000 0.00 0.00 42.67 4.20
1006 1030 2.281484 GAGGAGCGCAACCACCAA 60.281 61.111 21.98 0.00 0.00 3.67
1104 1149 2.529389 AAGGTCTGGAAGGGCCGT 60.529 61.111 0.00 0.00 40.66 5.68
1123 1168 3.099905 TGGTCTGATTGAGGTACCTGAG 58.900 50.000 22.10 7.12 0.00 3.35
1182 1227 1.078497 GATGGTGATGCCGTGGTGA 60.078 57.895 0.00 0.00 41.21 4.02
1252 1297 8.624701 ATGATTATTTCTTGCGTGATGAAAAG 57.375 30.769 0.00 0.00 32.93 2.27
1263 1308 7.426929 AGACGATGGTATGATTATTTCTTGC 57.573 36.000 0.00 0.00 0.00 4.01
1301 1346 0.539986 AACGGTCGCCAACATCCTAT 59.460 50.000 0.00 0.00 0.00 2.57
1302 1347 0.390603 CAACGGTCGCCAACATCCTA 60.391 55.000 0.00 0.00 0.00 2.94
1303 1348 1.671054 CAACGGTCGCCAACATCCT 60.671 57.895 0.00 0.00 0.00 3.24
1304 1349 2.867472 CAACGGTCGCCAACATCC 59.133 61.111 0.00 0.00 0.00 3.51
1305 1350 2.175811 GCAACGGTCGCCAACATC 59.824 61.111 0.00 0.00 0.00 3.06
1306 1351 2.593148 TGCAACGGTCGCCAACAT 60.593 55.556 0.00 0.00 0.00 2.71
1454 1499 3.026630 AGTCACGTTCACCATGTACAG 57.973 47.619 0.33 0.00 0.00 2.74
1960 2008 2.490270 CTTCCACCTTGCCTCCAGGG 62.490 65.000 0.00 0.00 43.48 4.45
1969 2017 2.628178 GGAACTTTTCCCTTCCACCTTG 59.372 50.000 0.00 0.00 44.30 3.61
1970 2018 2.958818 GGAACTTTTCCCTTCCACCTT 58.041 47.619 0.00 0.00 44.30 3.50
2058 2109 1.305219 TAGCGCACTTCACAATGCCC 61.305 55.000 11.47 0.00 38.69 5.36
2117 2168 6.885376 GTCACCCTAATCTATCCTAATCTCGA 59.115 42.308 0.00 0.00 0.00 4.04
2118 2169 6.183360 CGTCACCCTAATCTATCCTAATCTCG 60.183 46.154 0.00 0.00 0.00 4.04
2127 2178 7.864379 TCGTTTAATTCGTCACCCTAATCTATC 59.136 37.037 0.00 0.00 0.00 2.08
2132 2186 6.342906 TCATCGTTTAATTCGTCACCCTAAT 58.657 36.000 0.00 0.00 0.00 1.73
2139 2193 7.532546 GTCAACAAATCATCGTTTAATTCGTCA 59.467 33.333 0.00 0.00 0.00 4.35
2142 2196 6.734617 TCGTCAACAAATCATCGTTTAATTCG 59.265 34.615 0.00 0.00 0.00 3.34
2145 2199 6.013085 CGTCGTCAACAAATCATCGTTTAAT 58.987 36.000 0.00 0.00 0.00 1.40
2158 2212 1.588674 AAATCAGCCGTCGTCAACAA 58.411 45.000 0.00 0.00 0.00 2.83
2192 2262 1.340088 TAATATGGCGGGGCGTAAGA 58.660 50.000 0.00 0.00 43.02 2.10
2196 2266 2.224209 GCTATATAATATGGCGGGGCGT 60.224 50.000 0.00 0.00 0.00 5.68
2281 2358 8.707839 TCGGCATTTGATTCTTTTGTATTTTTC 58.292 29.630 0.00 0.00 0.00 2.29
2499 2594 4.074526 GTCGAGCCTGCCTGCAGA 62.075 66.667 20.29 0.00 46.30 4.26
2551 2646 1.829222 GGGAGAAATACCAGTCGACCA 59.171 52.381 13.01 0.00 0.00 4.02
2554 2649 3.134081 GGATTGGGAGAAATACCAGTCGA 59.866 47.826 0.00 0.00 42.48 4.20
2559 2654 3.309556 GGTTGGGATTGGGAGAAATACCA 60.310 47.826 0.00 0.00 46.84 3.25
2562 2657 4.231658 TGATGGTTGGGATTGGGAGAAATA 59.768 41.667 0.00 0.00 0.00 1.40
2632 2741 3.268965 GAGACAGCGTGAGTGGCGA 62.269 63.158 0.00 0.00 35.00 5.54
2664 2773 3.808218 TTGTGCAGGCCCCACTTCC 62.808 63.158 20.89 0.27 34.38 3.46
2744 2856 2.703536 TGGTTACCATCACTGACAGTGT 59.296 45.455 29.87 17.35 46.03 3.55
2770 2882 2.493278 GGTATGCTCCTGTTGTTGCATT 59.507 45.455 4.65 0.00 42.60 3.56
2772 2884 1.202867 TGGTATGCTCCTGTTGTTGCA 60.203 47.619 0.00 0.00 39.83 4.08
2799 2911 1.829970 GGGCATTTCAGGGCTAGGC 60.830 63.158 8.00 8.00 0.00 3.93
2800 2912 1.526917 CGGGCATTTCAGGGCTAGG 60.527 63.158 0.00 0.00 0.00 3.02
2801 2913 0.468226 TACGGGCATTTCAGGGCTAG 59.532 55.000 0.00 0.00 0.00 3.42
2802 2914 0.913205 TTACGGGCATTTCAGGGCTA 59.087 50.000 0.00 0.00 0.00 3.93
2809 2937 1.131693 CGGGAGTTTTACGGGCATTTC 59.868 52.381 0.00 0.00 0.00 2.17
2811 2939 1.310216 GCGGGAGTTTTACGGGCATT 61.310 55.000 0.00 0.00 0.00 3.56
2844 2972 2.598394 ACGCCAACAGCATGCCTT 60.598 55.556 15.66 2.84 42.53 4.35
2893 3021 4.152625 CTGCTTACTGCGCGGTGC 62.153 66.667 31.70 26.02 46.63 5.01
2900 3028 3.198489 GGCCTCGCTGCTTACTGC 61.198 66.667 0.00 0.00 43.25 4.40
2901 3029 1.520342 GAGGCCTCGCTGCTTACTG 60.520 63.158 19.06 0.00 0.00 2.74
2902 3030 1.984570 TGAGGCCTCGCTGCTTACT 60.985 57.895 27.43 0.00 0.00 2.24
2903 3031 1.811679 GTGAGGCCTCGCTGCTTAC 60.812 63.158 34.32 18.71 37.16 2.34
2904 3032 2.579201 GTGAGGCCTCGCTGCTTA 59.421 61.111 34.32 10.84 37.16 3.09
2910 3038 4.828925 GCTCCAGTGAGGCCTCGC 62.829 72.222 34.60 34.60 39.14 5.03
2911 3039 1.733402 CTAGCTCCAGTGAGGCCTCG 61.733 65.000 27.43 13.45 39.14 4.63
2912 3040 2.026945 GCTAGCTCCAGTGAGGCCTC 62.027 65.000 26.78 26.78 39.14 4.70
2913 3041 2.063378 GCTAGCTCCAGTGAGGCCT 61.063 63.158 3.86 3.86 39.14 5.19
2914 3042 2.503546 GCTAGCTCCAGTGAGGCC 59.496 66.667 7.70 0.00 39.14 5.19
2915 3043 2.503546 GGCTAGCTCCAGTGAGGC 59.496 66.667 15.72 0.00 39.14 4.70
2916 3044 1.687146 TGGGCTAGCTCCAGTGAGG 60.687 63.158 13.26 0.00 39.14 3.86
2917 3045 1.519719 GTGGGCTAGCTCCAGTGAG 59.480 63.158 21.10 0.00 41.84 3.51
2918 3046 1.990060 GGTGGGCTAGCTCCAGTGA 60.990 63.158 21.10 0.00 34.56 3.41
2919 3047 2.586792 GGTGGGCTAGCTCCAGTG 59.413 66.667 21.10 0.00 34.56 3.66
2920 3048 2.689034 GGGTGGGCTAGCTCCAGT 60.689 66.667 21.10 0.00 34.56 4.00
2921 3049 3.854669 CGGGTGGGCTAGCTCCAG 61.855 72.222 21.10 14.65 34.56 3.86
2932 3060 4.939368 TTGTTGTCGGCCGGGTGG 62.939 66.667 27.83 0.00 38.77 4.61
2933 3061 2.902846 TTTGTTGTCGGCCGGGTG 60.903 61.111 27.83 0.00 0.00 4.61
2934 3062 2.903350 GTTTGTTGTCGGCCGGGT 60.903 61.111 27.83 0.00 0.00 5.28
2935 3063 3.666253 GGTTTGTTGTCGGCCGGG 61.666 66.667 27.83 0.00 0.00 5.73
2936 3064 2.593436 AGGTTTGTTGTCGGCCGG 60.593 61.111 27.83 6.80 0.00 6.13
2937 3065 1.440938 TTGAGGTTTGTTGTCGGCCG 61.441 55.000 22.12 22.12 0.00 6.13
2938 3066 0.310854 CTTGAGGTTTGTTGTCGGCC 59.689 55.000 0.00 0.00 0.00 6.13
2939 3067 1.305201 TCTTGAGGTTTGTTGTCGGC 58.695 50.000 0.00 0.00 0.00 5.54
2940 3068 3.403038 AGATCTTGAGGTTTGTTGTCGG 58.597 45.455 0.00 0.00 0.00 4.79
2941 3069 5.470368 TCTAGATCTTGAGGTTTGTTGTCG 58.530 41.667 0.00 0.00 0.00 4.35
2942 3070 6.147985 GGTTCTAGATCTTGAGGTTTGTTGTC 59.852 42.308 0.00 0.00 0.00 3.18
2943 3071 5.998363 GGTTCTAGATCTTGAGGTTTGTTGT 59.002 40.000 0.00 0.00 0.00 3.32
2944 3072 5.120830 CGGTTCTAGATCTTGAGGTTTGTTG 59.879 44.000 0.00 0.00 0.00 3.33
2945 3073 5.011738 TCGGTTCTAGATCTTGAGGTTTGTT 59.988 40.000 0.00 0.00 0.00 2.83
2946 3074 4.527038 TCGGTTCTAGATCTTGAGGTTTGT 59.473 41.667 0.00 0.00 0.00 2.83
2947 3075 4.865365 GTCGGTTCTAGATCTTGAGGTTTG 59.135 45.833 0.00 0.00 0.00 2.93
2948 3076 4.380655 CGTCGGTTCTAGATCTTGAGGTTT 60.381 45.833 0.00 0.00 0.00 3.27
2949 3077 3.128938 CGTCGGTTCTAGATCTTGAGGTT 59.871 47.826 0.00 0.00 0.00 3.50
2950 3078 2.683867 CGTCGGTTCTAGATCTTGAGGT 59.316 50.000 0.00 0.00 0.00 3.85
2951 3079 2.943690 TCGTCGGTTCTAGATCTTGAGG 59.056 50.000 0.00 2.26 0.00 3.86
2952 3080 4.095185 AGTTCGTCGGTTCTAGATCTTGAG 59.905 45.833 0.00 0.00 0.00 3.02
2953 3081 4.008330 AGTTCGTCGGTTCTAGATCTTGA 58.992 43.478 0.00 0.41 0.00 3.02
2954 3082 4.358494 AGTTCGTCGGTTCTAGATCTTG 57.642 45.455 0.00 0.00 0.00 3.02
2955 3083 4.033817 CGTAGTTCGTCGGTTCTAGATCTT 59.966 45.833 0.00 0.00 34.52 2.40
2956 3084 3.555139 CGTAGTTCGTCGGTTCTAGATCT 59.445 47.826 0.00 0.00 34.52 2.75
2957 3085 3.553511 TCGTAGTTCGTCGGTTCTAGATC 59.446 47.826 0.00 0.00 40.80 2.75
2958 3086 3.525537 TCGTAGTTCGTCGGTTCTAGAT 58.474 45.455 0.00 0.00 40.80 1.98
2959 3087 2.959516 TCGTAGTTCGTCGGTTCTAGA 58.040 47.619 0.00 0.00 40.80 2.43
2960 3088 3.605406 CATCGTAGTTCGTCGGTTCTAG 58.395 50.000 0.00 0.00 40.80 2.43
2961 3089 2.223112 GCATCGTAGTTCGTCGGTTCTA 60.223 50.000 0.00 0.00 40.80 2.10
2962 3090 1.467035 GCATCGTAGTTCGTCGGTTCT 60.467 52.381 0.00 0.00 40.80 3.01
2963 3091 0.912528 GCATCGTAGTTCGTCGGTTC 59.087 55.000 0.00 0.00 40.80 3.62
2964 3092 0.457337 GGCATCGTAGTTCGTCGGTT 60.457 55.000 0.00 0.00 40.80 4.44
2965 3093 1.138247 GGCATCGTAGTTCGTCGGT 59.862 57.895 0.00 0.00 40.80 4.69
2966 3094 0.866061 CTGGCATCGTAGTTCGTCGG 60.866 60.000 0.00 0.00 40.80 4.79
2967 3095 0.098200 TCTGGCATCGTAGTTCGTCG 59.902 55.000 0.00 0.00 40.80 5.12
2968 3096 2.273370 TTCTGGCATCGTAGTTCGTC 57.727 50.000 0.00 0.00 40.80 4.20
2969 3097 2.736144 TTTCTGGCATCGTAGTTCGT 57.264 45.000 0.00 0.00 40.80 3.85
2970 3098 5.462068 TGATATTTTCTGGCATCGTAGTTCG 59.538 40.000 0.00 0.00 41.41 3.95
2971 3099 6.257849 TGTGATATTTTCTGGCATCGTAGTTC 59.742 38.462 0.00 0.00 0.00 3.01
2972 3100 6.112734 TGTGATATTTTCTGGCATCGTAGTT 58.887 36.000 0.00 0.00 0.00 2.24
2973 3101 5.670485 TGTGATATTTTCTGGCATCGTAGT 58.330 37.500 0.00 0.00 0.00 2.73
2974 3102 6.203530 ACATGTGATATTTTCTGGCATCGTAG 59.796 38.462 0.00 0.00 0.00 3.51
2975 3103 6.054941 ACATGTGATATTTTCTGGCATCGTA 58.945 36.000 0.00 0.00 0.00 3.43
2976 3104 4.883585 ACATGTGATATTTTCTGGCATCGT 59.116 37.500 0.00 0.00 0.00 3.73
2977 3105 5.428496 ACATGTGATATTTTCTGGCATCG 57.572 39.130 0.00 0.00 0.00 3.84
2978 3106 6.798482 TCAACATGTGATATTTTCTGGCATC 58.202 36.000 0.00 0.00 0.00 3.91
2979 3107 6.778834 TCAACATGTGATATTTTCTGGCAT 57.221 33.333 0.00 0.00 0.00 4.40
2980 3108 6.778834 ATCAACATGTGATATTTTCTGGCA 57.221 33.333 0.00 0.00 45.59 4.92
2981 3109 7.376866 CGTAATCAACATGTGATATTTTCTGGC 59.623 37.037 0.00 0.00 46.80 4.85
2982 3110 7.857389 CCGTAATCAACATGTGATATTTTCTGG 59.143 37.037 0.00 0.00 46.80 3.86
2983 3111 8.611757 TCCGTAATCAACATGTGATATTTTCTG 58.388 33.333 0.00 0.00 46.80 3.02
2984 3112 8.612619 GTCCGTAATCAACATGTGATATTTTCT 58.387 33.333 0.00 0.00 46.80 2.52
2985 3113 8.612619 AGTCCGTAATCAACATGTGATATTTTC 58.387 33.333 0.00 0.00 46.80 2.29
2986 3114 8.506168 AGTCCGTAATCAACATGTGATATTTT 57.494 30.769 0.00 0.00 46.80 1.82
2987 3115 9.778741 ATAGTCCGTAATCAACATGTGATATTT 57.221 29.630 0.00 0.00 46.80 1.40
2988 3116 9.778741 AATAGTCCGTAATCAACATGTGATATT 57.221 29.630 0.00 2.50 46.80 1.28
2992 3120 9.256477 GAATAATAGTCCGTAATCAACATGTGA 57.744 33.333 0.00 0.00 41.67 3.58
2993 3121 9.261180 AGAATAATAGTCCGTAATCAACATGTG 57.739 33.333 0.00 0.00 0.00 3.21
2997 3125 9.740239 GTGTAGAATAATAGTCCGTAATCAACA 57.260 33.333 0.00 0.00 0.00 3.33
2998 3126 9.962783 AGTGTAGAATAATAGTCCGTAATCAAC 57.037 33.333 0.00 0.00 0.00 3.18
2999 3127 9.961265 CAGTGTAGAATAATAGTCCGTAATCAA 57.039 33.333 0.00 0.00 0.00 2.57
3000 3128 8.080417 GCAGTGTAGAATAATAGTCCGTAATCA 58.920 37.037 0.00 0.00 0.00 2.57
3001 3129 7.541437 GGCAGTGTAGAATAATAGTCCGTAATC 59.459 40.741 0.00 0.00 0.00 1.75
3002 3130 7.232941 AGGCAGTGTAGAATAATAGTCCGTAAT 59.767 37.037 0.00 0.00 0.00 1.89
3003 3131 6.548622 AGGCAGTGTAGAATAATAGTCCGTAA 59.451 38.462 0.00 0.00 0.00 3.18
3004 3132 6.066690 AGGCAGTGTAGAATAATAGTCCGTA 58.933 40.000 0.00 0.00 0.00 4.02
3005 3133 4.894114 AGGCAGTGTAGAATAATAGTCCGT 59.106 41.667 0.00 0.00 0.00 4.69
3006 3134 5.455056 AGGCAGTGTAGAATAATAGTCCG 57.545 43.478 0.00 0.00 0.00 4.79
3007 3135 6.583562 ACAAGGCAGTGTAGAATAATAGTCC 58.416 40.000 0.00 0.00 0.00 3.85
3008 3136 7.265673 TGACAAGGCAGTGTAGAATAATAGTC 58.734 38.462 0.00 0.00 0.00 2.59
3009 3137 7.182817 TGACAAGGCAGTGTAGAATAATAGT 57.817 36.000 0.00 0.00 0.00 2.12
3010 3138 8.492673 TTTGACAAGGCAGTGTAGAATAATAG 57.507 34.615 0.00 0.00 0.00 1.73
3011 3139 8.726988 GTTTTGACAAGGCAGTGTAGAATAATA 58.273 33.333 0.00 0.00 0.00 0.98
3012 3140 7.448469 AGTTTTGACAAGGCAGTGTAGAATAAT 59.552 33.333 0.00 0.00 0.00 1.28
3013 3141 6.770785 AGTTTTGACAAGGCAGTGTAGAATAA 59.229 34.615 0.00 0.00 0.00 1.40
3014 3142 6.296026 AGTTTTGACAAGGCAGTGTAGAATA 58.704 36.000 0.00 0.00 0.00 1.75
3015 3143 5.133221 AGTTTTGACAAGGCAGTGTAGAAT 58.867 37.500 0.00 0.00 0.00 2.40
3016 3144 4.523083 AGTTTTGACAAGGCAGTGTAGAA 58.477 39.130 0.00 0.00 0.00 2.10
3017 3145 4.150897 AGTTTTGACAAGGCAGTGTAGA 57.849 40.909 0.00 0.00 0.00 2.59
3018 3146 4.814234 TGTAGTTTTGACAAGGCAGTGTAG 59.186 41.667 0.00 0.00 0.00 2.74
3019 3147 4.573201 GTGTAGTTTTGACAAGGCAGTGTA 59.427 41.667 0.00 0.00 0.00 2.90
3020 3148 3.377172 GTGTAGTTTTGACAAGGCAGTGT 59.623 43.478 0.00 0.00 0.00 3.55
3021 3149 3.243068 GGTGTAGTTTTGACAAGGCAGTG 60.243 47.826 0.00 0.00 0.00 3.66
3022 3150 2.949644 GGTGTAGTTTTGACAAGGCAGT 59.050 45.455 0.00 0.00 0.00 4.40
3023 3151 2.948979 TGGTGTAGTTTTGACAAGGCAG 59.051 45.455 0.00 0.00 0.00 4.85
3024 3152 3.006112 TGGTGTAGTTTTGACAAGGCA 57.994 42.857 0.00 0.00 0.00 4.75
3025 3153 3.568007 TGATGGTGTAGTTTTGACAAGGC 59.432 43.478 0.00 0.00 0.00 4.35
3026 3154 5.766150 TTGATGGTGTAGTTTTGACAAGG 57.234 39.130 0.00 0.00 0.00 3.61
3027 3155 6.475402 GGTTTTGATGGTGTAGTTTTGACAAG 59.525 38.462 0.00 0.00 0.00 3.16
3028 3156 6.071334 TGGTTTTGATGGTGTAGTTTTGACAA 60.071 34.615 0.00 0.00 0.00 3.18
3029 3157 5.419155 TGGTTTTGATGGTGTAGTTTTGACA 59.581 36.000 0.00 0.00 0.00 3.58
3030 3158 5.897050 TGGTTTTGATGGTGTAGTTTTGAC 58.103 37.500 0.00 0.00 0.00 3.18
3031 3159 6.723298 ATGGTTTTGATGGTGTAGTTTTGA 57.277 33.333 0.00 0.00 0.00 2.69
3032 3160 7.429633 TGTATGGTTTTGATGGTGTAGTTTTG 58.570 34.615 0.00 0.00 0.00 2.44
3033 3161 7.589958 TGTATGGTTTTGATGGTGTAGTTTT 57.410 32.000 0.00 0.00 0.00 2.43
3034 3162 7.589958 TTGTATGGTTTTGATGGTGTAGTTT 57.410 32.000 0.00 0.00 0.00 2.66
3035 3163 7.430441 GTTTGTATGGTTTTGATGGTGTAGTT 58.570 34.615 0.00 0.00 0.00 2.24
3036 3164 6.015772 GGTTTGTATGGTTTTGATGGTGTAGT 60.016 38.462 0.00 0.00 0.00 2.73
3037 3165 6.208599 AGGTTTGTATGGTTTTGATGGTGTAG 59.791 38.462 0.00 0.00 0.00 2.74
3038 3166 6.071984 AGGTTTGTATGGTTTTGATGGTGTA 58.928 36.000 0.00 0.00 0.00 2.90
3039 3167 4.898861 AGGTTTGTATGGTTTTGATGGTGT 59.101 37.500 0.00 0.00 0.00 4.16
3040 3168 5.467035 AGGTTTGTATGGTTTTGATGGTG 57.533 39.130 0.00 0.00 0.00 4.17
3041 3169 7.790782 ATTAGGTTTGTATGGTTTTGATGGT 57.209 32.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.