Multiple sequence alignment - TraesCS3A01G281800

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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 TraesCS3A01G281800 chr3A 100.000 3903 0 0 1 3903 510599980 510596078 0.000000e+00 7208.0
1 TraesCS3A01G281800 chr3A 87.500 168 15 5 3075 3239 7278254 7278090 5.150000e-44 189.0
2 TraesCS3A01G281800 chr3A 83.333 66 10 1 597 662 349154920 349154856 4.210000e-05 60.2
3 TraesCS3A01G281800 chr3B 92.243 2256 122 32 836 3083 507277525 507275315 0.000000e+00 3147.0
4 TraesCS3A01G281800 chr3B 94.397 464 23 3 3441 3903 507275034 507274573 0.000000e+00 710.0
5 TraesCS3A01G281800 chr3B 96.127 284 10 1 3205 3487 507275315 507275032 2.750000e-126 462.0
6 TraesCS3A01G281800 chr3B 87.037 54 5 2 437 489 13169378 13169430 4.210000e-05 60.2
7 TraesCS3A01G281800 chr3B 82.812 64 10 1 599 662 347996837 347996775 5.450000e-04 56.5
8 TraesCS3A01G281800 chr3D 93.053 2044 89 24 864 2902 389913801 389911806 0.000000e+00 2939.0
9 TraesCS3A01G281800 chr3D 96.132 698 26 1 3207 3903 389911659 389910962 0.000000e+00 1138.0
10 TraesCS3A01G281800 chr3D 91.250 800 46 3 1 799 389914575 389913799 0.000000e+00 1068.0
11 TraesCS3A01G281800 chr3D 92.053 151 6 2 2935 3085 389911800 389911656 1.420000e-49 207.0
12 TraesCS3A01G281800 chr3D 95.420 131 5 1 3082 3212 419877708 419877837 1.420000e-49 207.0
13 TraesCS3A01G281800 chr3D 93.382 136 9 0 3081 3216 496172883 496172748 6.610000e-48 202.0
14 TraesCS3A01G281800 chr3D 92.308 143 7 4 3078 3218 427451539 427451679 2.380000e-47 200.0
15 TraesCS3A01G281800 chr3D 82.418 91 13 3 522 611 133918896 133918808 4.180000e-10 76.8
16 TraesCS3A01G281800 chr3D 84.507 71 8 3 512 580 85010181 85010250 2.520000e-07 67.6
17 TraesCS3A01G281800 chr6A 94.444 720 35 3 2367 3085 74502012 74501297 0.000000e+00 1103.0
18 TraesCS3A01G281800 chrUn 91.250 160 11 2 3051 3210 11031814 11031658 8.490000e-52 215.0
19 TraesCS3A01G281800 chr7B 94.697 132 7 0 3077 3208 678632489 678632358 5.110000e-49 206.0
20 TraesCS3A01G281800 chr1A 94.697 132 7 0 3077 3208 287275006 287275137 5.110000e-49 206.0
21 TraesCS3A01G281800 chr1A 94.737 133 6 1 3076 3208 475456872 475457003 5.110000e-49 206.0
22 TraesCS3A01G281800 chr4A 92.361 144 9 2 3066 3209 147594659 147594800 1.840000e-48 204.0
23 TraesCS3A01G281800 chr4D 78.155 206 39 6 462 663 469197387 469197184 4.090000e-25 126.0
24 TraesCS3A01G281800 chr2D 76.959 217 39 10 432 642 36238999 36238788 3.190000e-21 113.0
25 TraesCS3A01G281800 chr2D 87.500 48 3 3 462 508 603134169 603134124 7.000000e-03 52.8
26 TraesCS3A01G281800 chr5D 71.759 432 99 15 3 427 396375829 396376244 2.480000e-17 100.0
27 TraesCS3A01G281800 chr1D 84.694 98 11 4 527 622 216532077 216532172 1.150000e-15 95.3
28 TraesCS3A01G281800 chr2B 76.744 172 22 14 459 615 729198703 729198871 3.230000e-11 80.5
29 TraesCS3A01G281800 chr4B 82.278 79 13 1 599 676 539501325 539501403 2.520000e-07 67.6


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 TraesCS3A01G281800 chr3A 510596078 510599980 3902 True 7208.000000 7208 100.000000 1 3903 1 chr3A.!!$R3 3902
1 TraesCS3A01G281800 chr3B 507274573 507277525 2952 True 1439.666667 3147 94.255667 836 3903 3 chr3B.!!$R2 3067
2 TraesCS3A01G281800 chr3D 389910962 389914575 3613 True 1338.000000 2939 93.122000 1 3903 4 chr3D.!!$R3 3902
3 TraesCS3A01G281800 chr6A 74501297 74502012 715 True 1103.000000 1103 94.444000 2367 3085 1 chr6A.!!$R1 718

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
787 789 0.037326 TGGTCGAGCTTCCACATGTC 60.037 55.0 16.64 0.0 0.0 3.06 F
975 982 0.182775 ACTCGGAGCCACAAAACCTT 59.817 50.0 4.58 0.0 0.0 3.50 F
1752 1773 0.749454 ATGATTGGCTTCGTGGGCTC 60.749 55.0 5.72 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1836 0.033781 GCTTGGGCATGCTTTTGTCA 59.966 50.0 18.92 4.19 38.54 3.58 R
1930 1951 1.217882 CCTGGAACGACAACAGACAC 58.782 55.0 0.00 0.00 34.21 3.67 R
3196 3227 0.034380 TAGCTCAGTACTCCTGCCGT 60.034 55.0 0.00 0.00 41.25 5.68 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
54 55 2.973899 AGCTGTTCGGCTCGTCAT 59.026 55.556 0.00 0.00 38.24 3.06
56 57 1.016130 AGCTGTTCGGCTCGTCATTG 61.016 55.000 0.00 0.00 38.24 2.82
72 73 3.261897 GTCATTGTCCTCCTCCTCTTTGA 59.738 47.826 0.00 0.00 0.00 2.69
134 135 3.712881 GCGAGGGCACGTGTGTTC 61.713 66.667 18.38 10.83 39.62 3.18
135 136 3.041940 CGAGGGCACGTGTGTTCC 61.042 66.667 18.38 13.40 0.00 3.62
136 137 2.426023 GAGGGCACGTGTGTTCCT 59.574 61.111 18.38 17.68 38.41 3.36
137 138 1.668151 GAGGGCACGTGTGTTCCTC 60.668 63.158 22.98 22.98 41.71 3.71
138 139 2.668550 GGGCACGTGTGTTCCTCC 60.669 66.667 18.38 7.50 0.00 4.30
139 140 2.426023 GGCACGTGTGTTCCTCCT 59.574 61.111 18.38 0.00 0.00 3.69
140 141 1.668151 GGCACGTGTGTTCCTCCTC 60.668 63.158 18.38 0.00 0.00 3.71
141 142 1.367840 GCACGTGTGTTCCTCCTCT 59.632 57.895 18.38 0.00 0.00 3.69
142 143 0.946221 GCACGTGTGTTCCTCCTCTG 60.946 60.000 18.38 0.00 0.00 3.35
143 144 0.946221 CACGTGTGTTCCTCCTCTGC 60.946 60.000 7.58 0.00 0.00 4.26
144 145 1.115930 ACGTGTGTTCCTCCTCTGCT 61.116 55.000 0.00 0.00 0.00 4.24
145 146 0.668706 CGTGTGTTCCTCCTCTGCTG 60.669 60.000 0.00 0.00 0.00 4.41
146 147 0.952984 GTGTGTTCCTCCTCTGCTGC 60.953 60.000 0.00 0.00 0.00 5.25
147 148 1.123861 TGTGTTCCTCCTCTGCTGCT 61.124 55.000 0.00 0.00 0.00 4.24
148 149 0.898320 GTGTTCCTCCTCTGCTGCTA 59.102 55.000 0.00 0.00 0.00 3.49
149 150 0.898320 TGTTCCTCCTCTGCTGCTAC 59.102 55.000 0.00 0.00 0.00 3.58
167 168 1.521457 CTGTATGATGCGGGCACGT 60.521 57.895 11.45 0.00 43.45 4.49
170 171 0.528901 GTATGATGCGGGCACGTACA 60.529 55.000 11.45 8.55 43.45 2.90
184 185 1.617357 ACGTACAACTTCCTCCTCCAC 59.383 52.381 0.00 0.00 0.00 4.02
189 190 1.415672 AACTTCCTCCTCCACGGCAA 61.416 55.000 0.00 0.00 0.00 4.52
278 279 2.097825 GCCCTCTACTTCTTACCACGA 58.902 52.381 0.00 0.00 0.00 4.35
287 288 3.069016 ACTTCTTACCACGATCACACACA 59.931 43.478 0.00 0.00 0.00 3.72
305 306 6.256539 CACACACATCCTTGTAGCACTAATAG 59.743 42.308 0.00 0.00 33.76 1.73
312 313 5.955959 TCCTTGTAGCACTAATAGTCCTTCA 59.044 40.000 0.00 0.00 0.00 3.02
366 367 3.854669 AGCTCCGGCGGATCCAAG 61.855 66.667 31.23 18.50 44.37 3.61
414 415 0.801067 CGTGAGACCGAATCCGAACC 60.801 60.000 0.00 0.00 38.22 3.62
480 481 4.575973 GGATCCGCTGCCTGCCAT 62.576 66.667 0.00 0.00 38.78 4.40
543 544 2.714793 AGTAAAGTGGCTAGGGTTTGGT 59.285 45.455 0.00 0.00 0.00 3.67
546 547 0.770557 AGTGGCTAGGGTTTGGTCCA 60.771 55.000 0.00 0.00 0.00 4.02
547 548 0.111639 GTGGCTAGGGTTTGGTCCAA 59.888 55.000 0.00 0.00 0.00 3.53
553 554 2.781681 AGGGTTTGGTCCAAGATACG 57.218 50.000 4.09 0.00 0.00 3.06
554 555 1.280998 AGGGTTTGGTCCAAGATACGG 59.719 52.381 4.09 0.00 0.00 4.02
644 645 5.549619 CCCAGGTCTTCCTATATTCATCCTT 59.450 44.000 0.00 0.00 43.07 3.36
663 664 8.668653 TCATCCTTAATTTAGGCTGGATATGAA 58.331 33.333 12.94 0.00 33.29 2.57
667 668 7.309438 CCTTAATTTAGGCTGGATATGAAAGGC 60.309 40.741 0.00 0.00 36.79 4.35
684 685 3.257561 CGCGAGTCAATCCAGGCG 61.258 66.667 0.00 0.00 37.56 5.52
698 699 3.057337 GGCGTATGAGGCCGGTAT 58.943 61.111 1.90 0.00 39.53 2.73
781 783 2.341846 AAAAGTTGGTCGAGCTTCCA 57.658 45.000 16.64 1.77 0.00 3.53
782 784 1.594331 AAAGTTGGTCGAGCTTCCAC 58.406 50.000 16.64 7.35 33.12 4.02
783 785 0.468226 AAGTTGGTCGAGCTTCCACA 59.532 50.000 16.64 0.00 33.12 4.17
784 786 0.687354 AGTTGGTCGAGCTTCCACAT 59.313 50.000 16.64 0.00 33.12 3.21
785 787 0.798776 GTTGGTCGAGCTTCCACATG 59.201 55.000 16.64 0.00 33.12 3.21
786 788 0.396435 TTGGTCGAGCTTCCACATGT 59.604 50.000 16.64 0.00 33.12 3.21
787 789 0.037326 TGGTCGAGCTTCCACATGTC 60.037 55.000 16.64 0.00 0.00 3.06
788 790 0.247736 GGTCGAGCTTCCACATGTCT 59.752 55.000 7.51 0.00 0.00 3.41
789 791 1.476891 GGTCGAGCTTCCACATGTCTA 59.523 52.381 7.51 0.00 0.00 2.59
790 792 2.480416 GGTCGAGCTTCCACATGTCTAG 60.480 54.545 7.51 0.00 0.00 2.43
791 793 2.164624 GTCGAGCTTCCACATGTCTAGT 59.835 50.000 0.00 0.00 0.00 2.57
792 794 2.423892 TCGAGCTTCCACATGTCTAGTC 59.576 50.000 0.00 0.00 0.00 2.59
793 795 2.792890 CGAGCTTCCACATGTCTAGTCG 60.793 54.545 0.00 0.00 0.00 4.18
794 796 2.423892 GAGCTTCCACATGTCTAGTCGA 59.576 50.000 0.00 0.00 0.00 4.20
795 797 2.425312 AGCTTCCACATGTCTAGTCGAG 59.575 50.000 0.00 0.00 0.00 4.04
796 798 2.803451 CTTCCACATGTCTAGTCGAGC 58.197 52.381 0.00 0.00 0.00 5.03
797 799 1.834188 TCCACATGTCTAGTCGAGCA 58.166 50.000 0.00 0.00 0.00 4.26
798 800 1.745653 TCCACATGTCTAGTCGAGCAG 59.254 52.381 0.00 0.00 0.00 4.24
799 801 1.745653 CCACATGTCTAGTCGAGCAGA 59.254 52.381 0.00 0.00 0.00 4.26
800 802 2.164422 CCACATGTCTAGTCGAGCAGAA 59.836 50.000 0.00 0.00 0.00 3.02
801 803 3.175152 CACATGTCTAGTCGAGCAGAAC 58.825 50.000 0.00 0.00 0.00 3.01
802 804 2.820197 ACATGTCTAGTCGAGCAGAACA 59.180 45.455 0.00 0.83 0.00 3.18
803 805 3.119673 ACATGTCTAGTCGAGCAGAACAG 60.120 47.826 0.00 0.00 0.00 3.16
804 806 1.813178 TGTCTAGTCGAGCAGAACAGG 59.187 52.381 0.00 0.00 0.00 4.00
805 807 1.813786 GTCTAGTCGAGCAGAACAGGT 59.186 52.381 0.00 0.00 0.00 4.00
806 808 1.813178 TCTAGTCGAGCAGAACAGGTG 59.187 52.381 0.00 0.00 0.00 4.00
807 809 1.813178 CTAGTCGAGCAGAACAGGTGA 59.187 52.381 0.00 0.00 0.00 4.02
808 810 1.261480 AGTCGAGCAGAACAGGTGAT 58.739 50.000 0.00 0.00 0.00 3.06
809 811 1.067283 AGTCGAGCAGAACAGGTGATG 60.067 52.381 0.00 0.00 0.00 3.07
810 812 0.390340 TCGAGCAGAACAGGTGATGC 60.390 55.000 1.96 1.96 38.97 3.91
812 814 3.547567 AGCAGAACAGGTGATGCTC 57.452 52.632 5.97 0.00 45.57 4.26
813 815 0.390866 AGCAGAACAGGTGATGCTCG 60.391 55.000 5.97 0.00 45.57 5.03
814 816 0.390340 GCAGAACAGGTGATGCTCGA 60.390 55.000 2.80 0.00 35.78 4.04
815 817 1.354040 CAGAACAGGTGATGCTCGAC 58.646 55.000 0.00 0.00 0.00 4.20
816 818 0.969149 AGAACAGGTGATGCTCGACA 59.031 50.000 0.00 0.00 0.00 4.35
817 819 1.071605 GAACAGGTGATGCTCGACAC 58.928 55.000 0.00 0.00 36.44 3.67
821 823 3.479370 GTGATGCTCGACACCAGC 58.521 61.111 0.00 0.00 37.40 4.85
869 876 6.076981 AGCTTGGACAGATAAAACAGTTTG 57.923 37.500 0.00 0.00 0.00 2.93
893 900 0.998145 AGCTCATCTTCCTTTGCCCT 59.002 50.000 0.00 0.00 0.00 5.19
896 903 2.641305 CTCATCTTCCTTTGCCCTCAG 58.359 52.381 0.00 0.00 0.00 3.35
909 916 2.909006 TGCCCTCAGAAACATCTCTCTT 59.091 45.455 0.00 0.00 0.00 2.85
975 982 0.182775 ACTCGGAGCCACAAAACCTT 59.817 50.000 4.58 0.00 0.00 3.50
1062 1070 3.168528 AGAACACCCCGCACACCT 61.169 61.111 0.00 0.00 0.00 4.00
1154 1162 2.509336 CTCCGCCGCAAGAACGAT 60.509 61.111 0.00 0.00 38.71 3.73
1410 1421 2.800250 AGGTCCTTTTTCCTGCATCTG 58.200 47.619 0.00 0.00 32.29 2.90
1414 1425 3.379688 GTCCTTTTTCCTGCATCTGATCC 59.620 47.826 0.00 0.00 0.00 3.36
1426 1438 3.131755 GCATCTGATCCCCCTTTTGAAAG 59.868 47.826 0.00 0.00 35.79 2.62
1431 1443 2.891191 TCCCCCTTTTGAAAGCGTAT 57.109 45.000 0.00 0.00 34.69 3.06
1432 1444 2.442413 TCCCCCTTTTGAAAGCGTATG 58.558 47.619 0.00 0.00 34.69 2.39
1437 1449 5.478407 CCCCTTTTGAAAGCGTATGAAAAT 58.522 37.500 0.00 0.00 34.69 1.82
1438 1450 5.348451 CCCCTTTTGAAAGCGTATGAAAATG 59.652 40.000 0.00 0.00 34.69 2.32
1440 1452 6.155827 CCTTTTGAAAGCGTATGAAAATGGA 58.844 36.000 0.00 0.00 34.69 3.41
1444 1456 6.325919 TGAAAGCGTATGAAAATGGAAGTT 57.674 33.333 0.00 0.00 0.00 2.66
1446 1458 6.206634 TGAAAGCGTATGAAAATGGAAGTTCT 59.793 34.615 2.25 0.00 0.00 3.01
1447 1459 7.389330 TGAAAGCGTATGAAAATGGAAGTTCTA 59.611 33.333 2.25 0.00 0.00 2.10
1448 1460 7.681939 AAGCGTATGAAAATGGAAGTTCTAA 57.318 32.000 2.25 0.00 0.00 2.10
1483 1495 4.278310 ACTGGGTTATGATTAAGTTGGGC 58.722 43.478 0.00 0.00 0.00 5.36
1540 1552 5.119898 CAGTCTTCAGTGTAGATCAAACTGC 59.880 44.000 14.36 4.55 40.89 4.40
1541 1553 4.991056 GTCTTCAGTGTAGATCAAACTGCA 59.009 41.667 14.36 6.23 40.89 4.41
1550 1562 7.039504 AGTGTAGATCAAACTGCAAAATCCAAT 60.040 33.333 0.00 0.00 34.67 3.16
1567 1580 8.668510 AAATCCAATTCAGTAGTGTGCTATAG 57.331 34.615 0.00 0.00 0.00 1.31
1571 1584 8.414003 TCCAATTCAGTAGTGTGCTATAGTAAG 58.586 37.037 0.84 0.00 0.00 2.34
1572 1585 8.414003 CCAATTCAGTAGTGTGCTATAGTAAGA 58.586 37.037 0.84 0.00 0.00 2.10
1573 1586 9.803315 CAATTCAGTAGTGTGCTATAGTAAGAA 57.197 33.333 0.84 0.00 0.00 2.52
1619 1633 5.583854 ACAGTTAGCTAATCTCACAATGCAG 59.416 40.000 9.88 0.00 0.00 4.41
1622 1636 2.681848 AGCTAATCTCACAATGCAGTGC 59.318 45.455 15.18 8.58 39.35 4.40
1623 1637 2.223433 GCTAATCTCACAATGCAGTGCC 60.223 50.000 15.18 0.00 39.35 5.01
1626 1640 1.456296 TCTCACAATGCAGTGCCATC 58.544 50.000 15.18 0.00 39.35 3.51
1627 1641 1.003928 TCTCACAATGCAGTGCCATCT 59.996 47.619 15.18 0.00 39.35 2.90
1628 1642 1.816835 CTCACAATGCAGTGCCATCTT 59.183 47.619 15.18 0.00 39.35 2.40
1629 1643 1.542472 TCACAATGCAGTGCCATCTTG 59.458 47.619 15.18 12.95 39.35 3.02
1630 1644 0.892755 ACAATGCAGTGCCATCTTGG 59.107 50.000 15.18 0.00 41.55 3.61
1631 1645 1.179152 CAATGCAGTGCCATCTTGGA 58.821 50.000 13.72 0.00 40.96 3.53
1632 1646 1.754803 CAATGCAGTGCCATCTTGGAT 59.245 47.619 13.72 0.00 40.96 3.41
1633 1647 2.953648 CAATGCAGTGCCATCTTGGATA 59.046 45.455 13.72 0.00 40.96 2.59
1634 1648 2.042686 TGCAGTGCCATCTTGGATAC 57.957 50.000 13.72 0.00 40.96 2.24
1635 1649 1.561076 TGCAGTGCCATCTTGGATACT 59.439 47.619 13.72 0.00 40.96 2.12
1636 1650 2.025981 TGCAGTGCCATCTTGGATACTT 60.026 45.455 13.72 0.00 40.96 2.24
1637 1651 3.019564 GCAGTGCCATCTTGGATACTTT 58.980 45.455 2.85 0.00 40.96 2.66
1638 1652 3.181493 GCAGTGCCATCTTGGATACTTTG 60.181 47.826 2.85 0.00 40.96 2.77
1639 1653 4.264253 CAGTGCCATCTTGGATACTTTGA 58.736 43.478 0.00 0.00 40.96 2.69
1640 1654 4.095483 CAGTGCCATCTTGGATACTTTGAC 59.905 45.833 0.00 0.00 40.96 3.18
1641 1655 3.063997 GTGCCATCTTGGATACTTTGACG 59.936 47.826 0.00 0.00 40.96 4.35
1642 1656 3.055458 TGCCATCTTGGATACTTTGACGA 60.055 43.478 0.00 0.00 40.96 4.20
1643 1657 3.557595 GCCATCTTGGATACTTTGACGAG 59.442 47.826 0.00 0.00 40.96 4.18
1644 1658 4.759782 CCATCTTGGATACTTTGACGAGT 58.240 43.478 0.00 0.00 40.96 4.18
1645 1659 4.568359 CCATCTTGGATACTTTGACGAGTG 59.432 45.833 0.00 0.00 40.96 3.51
1646 1660 4.866508 TCTTGGATACTTTGACGAGTGT 57.133 40.909 0.00 0.00 37.61 3.55
1647 1661 5.970317 TCTTGGATACTTTGACGAGTGTA 57.030 39.130 0.00 0.00 37.61 2.90
1648 1662 6.335471 TCTTGGATACTTTGACGAGTGTAA 57.665 37.500 0.00 0.00 37.61 2.41
1653 1674 6.209192 TGGATACTTTGACGAGTGTAAACCTA 59.791 38.462 0.00 0.00 37.61 3.08
1668 1689 6.793680 GTGTAAACCTAACACTTTACGATTGC 59.206 38.462 0.00 0.00 43.13 3.56
1672 1693 4.451096 ACCTAACACTTTACGATTGCACTG 59.549 41.667 0.00 0.00 0.00 3.66
1674 1695 5.178623 CCTAACACTTTACGATTGCACTGAA 59.821 40.000 0.00 0.00 0.00 3.02
1680 1701 5.700832 ACTTTACGATTGCACTGAATTCTCA 59.299 36.000 7.05 0.00 0.00 3.27
1688 1709 1.057822 CTGAATTCTCACACGCGCG 59.942 57.895 30.96 30.96 0.00 6.86
1713 1734 2.567615 GTCCTCCTTTCAGGCTCTTGTA 59.432 50.000 0.00 0.00 34.61 2.41
1734 1755 2.439507 ACCGGATCTATTGCTCAACCAT 59.560 45.455 9.46 0.00 0.00 3.55
1752 1773 0.749454 ATGATTGGCTTCGTGGGCTC 60.749 55.000 5.72 0.00 0.00 4.70
1815 1836 6.206243 GCTCATATGCATGGTATCAGTTTCTT 59.794 38.462 10.16 0.00 32.61 2.52
2103 2124 0.882042 ACTGTTTCTGCCTGAGCGTG 60.882 55.000 0.00 0.00 44.31 5.34
2112 2133 0.438830 GCCTGAGCGTGTTCTTAACG 59.561 55.000 0.00 0.00 43.81 3.18
2156 2179 8.939929 CAACTCATGTTATGTTATGTCTCACTT 58.060 33.333 0.00 0.00 34.60 3.16
2157 2180 9.507329 AACTCATGTTATGTTATGTCTCACTTT 57.493 29.630 0.00 0.00 34.15 2.66
2243 2266 8.953313 AGTCTCTTAACTTCTAGCTCTACTTTC 58.047 37.037 0.00 0.00 0.00 2.62
2274 2298 6.456795 AGCTAAGCATTTTTCTAATCCCAC 57.543 37.500 0.00 0.00 0.00 4.61
2280 2304 6.963322 AGCATTTTTCTAATCCCACTCTAGT 58.037 36.000 0.00 0.00 0.00 2.57
2489 2514 2.185004 TCAGGTTAGTTCTTGCTGCC 57.815 50.000 0.00 0.00 0.00 4.85
2502 2527 2.574006 TGCTGCCACTCAAAATCTCT 57.426 45.000 0.00 0.00 0.00 3.10
2512 2537 6.238593 GCCACTCAAAATCTCTGATGATTACC 60.239 42.308 0.00 0.00 35.82 2.85
2616 2642 6.388689 TGAAGGGGCTTCTTTCCTATTATACA 59.611 38.462 0.00 0.00 40.73 2.29
2728 2754 4.267928 CGGTCGATGGAGAAATTACAGTTC 59.732 45.833 0.00 0.00 0.00 3.01
2984 3011 6.040166 CAGGTTCCAGCATCTTTAATAGCATT 59.960 38.462 0.00 0.00 0.00 3.56
2985 3012 6.040166 AGGTTCCAGCATCTTTAATAGCATTG 59.960 38.462 0.00 0.00 0.00 2.82
2986 3013 5.443185 TCCAGCATCTTTAATAGCATTGC 57.557 39.130 0.00 0.00 0.00 3.56
3024 3052 8.044309 TCGTGGTCAATATTATCTTTTCCTGAA 58.956 33.333 0.00 0.00 0.00 3.02
3062 3090 6.321181 TCACAAACTGTTCCTTAAGCAAAGAT 59.679 34.615 0.00 0.00 37.38 2.40
3088 3119 8.147244 ACTTGTTTCACAGTATAATACTCCCT 57.853 34.615 0.00 0.00 36.76 4.20
3089 3120 8.258708 ACTTGTTTCACAGTATAATACTCCCTC 58.741 37.037 0.00 0.00 36.76 4.30
3090 3121 7.973048 TGTTTCACAGTATAATACTCCCTCT 57.027 36.000 0.00 0.00 36.76 3.69
3091 3122 7.782049 TGTTTCACAGTATAATACTCCCTCTG 58.218 38.462 0.00 0.00 36.76 3.35
3092 3123 7.399191 TGTTTCACAGTATAATACTCCCTCTGT 59.601 37.037 0.00 0.00 36.76 3.41
3093 3124 7.584122 TTCACAGTATAATACTCCCTCTGTC 57.416 40.000 0.00 0.00 36.76 3.51
3094 3125 6.069331 TCACAGTATAATACTCCCTCTGTCC 58.931 44.000 0.00 0.00 36.76 4.02
3095 3126 5.244178 CACAGTATAATACTCCCTCTGTCCC 59.756 48.000 0.00 0.00 36.76 4.46
3096 3127 5.103215 ACAGTATAATACTCCCTCTGTCCCA 60.103 44.000 0.00 0.00 36.76 4.37
3097 3128 5.839063 CAGTATAATACTCCCTCTGTCCCAA 59.161 44.000 0.00 0.00 36.76 4.12
3098 3129 6.326583 CAGTATAATACTCCCTCTGTCCCAAA 59.673 42.308 0.00 0.00 36.76 3.28
3099 3130 6.906901 AGTATAATACTCCCTCTGTCCCAAAA 59.093 38.462 0.00 0.00 32.47 2.44
3100 3131 6.848562 ATAATACTCCCTCTGTCCCAAAAT 57.151 37.500 0.00 0.00 0.00 1.82
3101 3132 5.536497 AATACTCCCTCTGTCCCAAAATT 57.464 39.130 0.00 0.00 0.00 1.82
3102 3133 3.441500 ACTCCCTCTGTCCCAAAATTC 57.558 47.619 0.00 0.00 0.00 2.17
3103 3134 2.989571 ACTCCCTCTGTCCCAAAATTCT 59.010 45.455 0.00 0.00 0.00 2.40
3104 3135 3.399305 ACTCCCTCTGTCCCAAAATTCTT 59.601 43.478 0.00 0.00 0.00 2.52
3105 3136 3.760684 CTCCCTCTGTCCCAAAATTCTTG 59.239 47.826 0.00 0.00 0.00 3.02
3106 3137 3.140144 TCCCTCTGTCCCAAAATTCTTGT 59.860 43.478 0.00 0.00 0.00 3.16
3107 3138 3.507622 CCCTCTGTCCCAAAATTCTTGTC 59.492 47.826 0.00 0.00 0.00 3.18
3108 3139 4.401925 CCTCTGTCCCAAAATTCTTGTCT 58.598 43.478 0.00 0.00 0.00 3.41
3109 3140 4.829492 CCTCTGTCCCAAAATTCTTGTCTT 59.171 41.667 0.00 0.00 0.00 3.01
3110 3141 6.003950 CCTCTGTCCCAAAATTCTTGTCTTA 58.996 40.000 0.00 0.00 0.00 2.10
3111 3142 6.150140 CCTCTGTCCCAAAATTCTTGTCTTAG 59.850 42.308 0.00 0.00 0.00 2.18
3112 3143 6.837312 TCTGTCCCAAAATTCTTGTCTTAGA 58.163 36.000 0.00 0.00 0.00 2.10
3113 3144 7.461749 TCTGTCCCAAAATTCTTGTCTTAGAT 58.538 34.615 0.00 0.00 0.00 1.98
3114 3145 7.944554 TCTGTCCCAAAATTCTTGTCTTAGATT 59.055 33.333 0.00 0.00 0.00 2.40
3115 3146 8.477419 TGTCCCAAAATTCTTGTCTTAGATTT 57.523 30.769 0.00 0.00 0.00 2.17
3116 3147 8.359642 TGTCCCAAAATTCTTGTCTTAGATTTG 58.640 33.333 0.00 0.00 29.84 2.32
3117 3148 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3118 3149 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3119 3150 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3127 3158 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
3128 3159 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
3130 3161 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
3131 3162 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
3138 3169 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
3139 3170 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
3140 3171 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
3141 3172 8.638873 TGTCTAAATACGGATGTATCAAGTCAT 58.361 33.333 0.00 0.00 40.42 3.06
3142 3173 8.916654 GTCTAAATACGGATGTATCAAGTCATG 58.083 37.037 0.00 0.00 40.42 3.07
3143 3174 8.638873 TCTAAATACGGATGTATCAAGTCATGT 58.361 33.333 0.00 0.00 40.42 3.21
3144 3175 9.261180 CTAAATACGGATGTATCAAGTCATGTT 57.739 33.333 0.00 0.00 40.42 2.71
3145 3176 8.506168 AAATACGGATGTATCAAGTCATGTTT 57.494 30.769 0.00 0.00 40.42 2.83
3146 3177 8.506168 AATACGGATGTATCAAGTCATGTTTT 57.494 30.769 0.00 0.00 40.42 2.43
3147 3178 9.607988 AATACGGATGTATCAAGTCATGTTTTA 57.392 29.630 0.00 0.00 40.42 1.52
3148 3179 7.539712 ACGGATGTATCAAGTCATGTTTTAG 57.460 36.000 0.00 0.00 0.00 1.85
3149 3180 7.103641 ACGGATGTATCAAGTCATGTTTTAGT 58.896 34.615 0.00 0.00 0.00 2.24
3150 3181 8.255206 ACGGATGTATCAAGTCATGTTTTAGTA 58.745 33.333 0.00 0.00 0.00 1.82
3151 3182 8.540492 CGGATGTATCAAGTCATGTTTTAGTAC 58.460 37.037 0.00 0.00 0.00 2.73
3152 3183 9.601217 GGATGTATCAAGTCATGTTTTAGTACT 57.399 33.333 0.00 0.00 0.00 2.73
3173 3204 9.993454 AGTACTACATACATTCGTATCTAGACA 57.007 33.333 0.00 0.00 36.11 3.41
3183 3214 9.953697 ACATTCGTATCTAGACAAATCTAAGAC 57.046 33.333 0.00 0.00 36.98 3.01
3184 3215 9.952188 CATTCGTATCTAGACAAATCTAAGACA 57.048 33.333 0.00 0.00 36.98 3.41
3187 3218 9.392259 TCGTATCTAGACAAATCTAAGACAAGA 57.608 33.333 0.00 0.00 36.98 3.02
3195 3226 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3196 3227 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3197 3228 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3198 3229 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3199 3230 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3200 3231 1.886542 AGACAAGAATTTTGGGACGGC 59.113 47.619 0.00 0.00 0.00 5.68
3201 3232 1.611491 GACAAGAATTTTGGGACGGCA 59.389 47.619 0.00 0.00 0.00 5.69
3202 3233 1.613437 ACAAGAATTTTGGGACGGCAG 59.387 47.619 0.00 0.00 0.00 4.85
3203 3234 1.067635 CAAGAATTTTGGGACGGCAGG 60.068 52.381 0.00 0.00 0.00 4.85
3204 3235 0.404040 AGAATTTTGGGACGGCAGGA 59.596 50.000 0.00 0.00 0.00 3.86
3205 3236 0.811281 GAATTTTGGGACGGCAGGAG 59.189 55.000 0.00 0.00 0.00 3.69
3206 3237 0.112412 AATTTTGGGACGGCAGGAGT 59.888 50.000 0.00 0.00 0.00 3.85
3207 3238 0.988832 ATTTTGGGACGGCAGGAGTA 59.011 50.000 0.00 0.00 0.00 2.59
3208 3239 0.035739 TTTTGGGACGGCAGGAGTAC 59.964 55.000 0.00 0.00 0.00 2.73
3209 3240 0.834687 TTTGGGACGGCAGGAGTACT 60.835 55.000 0.00 0.00 0.00 2.73
3222 3253 3.221771 AGGAGTACTGAGCTATGCTGAG 58.778 50.000 0.00 4.59 45.01 3.35
3250 3281 7.669722 AGAAAACCATTTATTAGTGAAGCCTCA 59.330 33.333 0.00 0.00 0.00 3.86
3254 3285 5.529060 CCATTTATTAGTGAAGCCTCAGGTC 59.471 44.000 0.00 0.00 30.14 3.85
3404 3435 4.017808 AGCTACAGTCTACAAGGTACAGG 58.982 47.826 0.00 0.00 0.00 4.00
3655 3731 4.929819 TTAAGCAGGGTTCAAAAACTCC 57.070 40.909 0.00 0.00 36.44 3.85
3657 3733 0.313987 GCAGGGTTCAAAAACTCCGG 59.686 55.000 0.00 0.00 36.44 5.14
3658 3734 1.975660 CAGGGTTCAAAAACTCCGGA 58.024 50.000 2.93 2.93 36.44 5.14
3720 3796 2.293122 GCTGTGCTGTGTTCAAATACCA 59.707 45.455 0.00 0.00 0.00 3.25
3783 3860 6.423604 AGCCGTTCCAAACTATTCAAAATTTG 59.576 34.615 0.00 0.00 32.89 2.32
3844 3921 1.606668 CCTCTTTTTGGCACTGCGTTA 59.393 47.619 0.00 0.00 0.00 3.18
3853 3930 1.201987 GGCACTGCGTTAATGTTACCG 60.202 52.381 0.00 0.00 0.00 4.02
3870 3947 8.806177 ATGTTACCGTTTCCTTTTTCAAATAC 57.194 30.769 0.00 0.00 0.00 1.89
3871 3948 7.998580 TGTTACCGTTTCCTTTTTCAAATACT 58.001 30.769 0.00 0.00 0.00 2.12
3895 3972 8.360390 ACTTTTGGTTTCCTCATAGAAATTGTC 58.640 33.333 0.00 0.00 38.01 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 0.716108 GACAATGACGAGCCGAACAG 59.284 55.000 1.50 0.00 0.00 3.16
46 47 0.179097 GGAGGAGGACAATGACGAGC 60.179 60.000 0.00 0.00 0.00 5.03
48 49 1.006043 AGAGGAGGAGGACAATGACGA 59.994 52.381 0.00 0.00 0.00 4.20
52 53 3.871485 CTCAAAGAGGAGGAGGACAATG 58.129 50.000 0.00 0.00 0.00 2.82
72 73 3.790437 CATGGCCGGACTGCTCCT 61.790 66.667 9.82 0.00 33.79 3.69
84 85 4.740822 AGGGGTTCGTGCCATGGC 62.741 66.667 30.54 30.54 42.35 4.40
128 129 1.123861 AGCAGCAGAGGAGGAACACA 61.124 55.000 0.00 0.00 0.00 3.72
129 130 0.898320 TAGCAGCAGAGGAGGAACAC 59.102 55.000 0.00 0.00 0.00 3.32
130 131 0.898320 GTAGCAGCAGAGGAGGAACA 59.102 55.000 0.00 0.00 0.00 3.18
131 132 1.134848 CAGTAGCAGCAGAGGAGGAAC 60.135 57.143 0.00 0.00 0.00 3.62
132 133 1.189752 CAGTAGCAGCAGAGGAGGAA 58.810 55.000 0.00 0.00 0.00 3.36
133 134 0.040351 ACAGTAGCAGCAGAGGAGGA 59.960 55.000 0.00 0.00 0.00 3.71
134 135 1.769026 TACAGTAGCAGCAGAGGAGG 58.231 55.000 0.00 0.00 0.00 4.30
135 136 2.954989 TCATACAGTAGCAGCAGAGGAG 59.045 50.000 0.00 0.00 0.00 3.69
136 137 3.018423 TCATACAGTAGCAGCAGAGGA 57.982 47.619 0.00 0.00 0.00 3.71
137 138 3.651206 CATCATACAGTAGCAGCAGAGG 58.349 50.000 0.00 0.00 0.00 3.69
138 139 3.058450 GCATCATACAGTAGCAGCAGAG 58.942 50.000 0.00 0.00 0.00 3.35
139 140 2.544486 CGCATCATACAGTAGCAGCAGA 60.544 50.000 0.00 0.00 0.00 4.26
140 141 1.791204 CGCATCATACAGTAGCAGCAG 59.209 52.381 0.00 0.00 0.00 4.24
141 142 1.538849 CCGCATCATACAGTAGCAGCA 60.539 52.381 0.00 0.00 0.00 4.41
142 143 1.143305 CCGCATCATACAGTAGCAGC 58.857 55.000 0.00 0.00 0.00 5.25
143 144 1.788258 CCCGCATCATACAGTAGCAG 58.212 55.000 0.00 0.00 0.00 4.24
144 145 0.249868 GCCCGCATCATACAGTAGCA 60.250 55.000 0.00 0.00 0.00 3.49
145 146 0.249868 TGCCCGCATCATACAGTAGC 60.250 55.000 0.00 0.00 0.00 3.58
146 147 1.502231 GTGCCCGCATCATACAGTAG 58.498 55.000 0.00 0.00 0.00 2.57
147 148 0.249280 CGTGCCCGCATCATACAGTA 60.249 55.000 0.00 0.00 0.00 2.74
148 149 1.521457 CGTGCCCGCATCATACAGT 60.521 57.895 0.00 0.00 0.00 3.55
149 150 0.249280 TACGTGCCCGCATCATACAG 60.249 55.000 0.00 0.00 37.70 2.74
167 168 1.263356 CCGTGGAGGAGGAAGTTGTA 58.737 55.000 0.00 0.00 45.00 2.41
170 171 1.415672 TTGCCGTGGAGGAGGAAGTT 61.416 55.000 0.00 0.00 45.00 2.66
255 256 0.822164 GGTAAGAAGTAGAGGGCGCA 59.178 55.000 10.83 0.00 0.00 6.09
278 279 3.008375 AGTGCTACAAGGATGTGTGTGAT 59.992 43.478 0.00 0.00 40.84 3.06
287 288 6.611642 TGAAGGACTATTAGTGCTACAAGGAT 59.388 38.462 17.00 1.26 46.56 3.24
305 306 0.108138 CCATCTCCGGTGTGAAGGAC 60.108 60.000 0.00 0.00 32.33 3.85
312 313 3.771160 GCCGACCATCTCCGGTGT 61.771 66.667 0.00 0.00 46.84 4.16
329 330 1.137825 GAAGCTCGAGGTCCGTCTG 59.862 63.158 18.90 0.00 39.75 3.51
457 458 2.136878 AGGCAGCGGATCCGATTCT 61.137 57.895 37.64 25.90 42.83 2.40
460 461 4.615815 GCAGGCAGCGGATCCGAT 62.616 66.667 37.64 30.27 42.83 4.18
498 499 1.323271 CCACTCCGCCTCAAGCTCTA 61.323 60.000 0.00 0.00 40.39 2.43
518 519 1.907255 ACCCTAGCCACTTTACTCACC 59.093 52.381 0.00 0.00 0.00 4.02
543 544 3.371034 TCCTTCACATCCGTATCTTGGA 58.629 45.455 0.00 0.00 40.46 3.53
546 547 8.816894 ACATATATTCCTTCACATCCGTATCTT 58.183 33.333 0.00 0.00 0.00 2.40
547 548 8.253810 CACATATATTCCTTCACATCCGTATCT 58.746 37.037 0.00 0.00 0.00 1.98
553 554 5.222130 ACCCCACATATATTCCTTCACATCC 60.222 44.000 0.00 0.00 0.00 3.51
554 555 5.880901 ACCCCACATATATTCCTTCACATC 58.119 41.667 0.00 0.00 0.00 3.06
644 645 5.705441 CGCCTTTCATATCCAGCCTAAATTA 59.295 40.000 0.00 0.00 0.00 1.40
663 664 1.448540 CTGGATTGACTCGCGCCTT 60.449 57.895 0.00 0.00 0.00 4.35
667 668 2.607668 TACGCCTGGATTGACTCGCG 62.608 60.000 0.00 0.00 44.78 5.87
684 685 2.102588 ACTTCACATACCGGCCTCATAC 59.897 50.000 0.00 0.00 0.00 2.39
698 699 4.974645 ACCCAATCTAGACAACTTCACA 57.025 40.909 0.00 0.00 0.00 3.58
763 765 1.134220 TGTGGAAGCTCGACCAACTTT 60.134 47.619 8.47 0.00 37.94 2.66
764 766 0.468226 TGTGGAAGCTCGACCAACTT 59.532 50.000 8.47 0.00 37.94 2.66
765 767 0.687354 ATGTGGAAGCTCGACCAACT 59.313 50.000 8.47 0.00 37.94 3.16
766 768 0.798776 CATGTGGAAGCTCGACCAAC 59.201 55.000 8.47 5.11 37.94 3.77
767 769 0.396435 ACATGTGGAAGCTCGACCAA 59.604 50.000 0.00 1.99 37.94 3.67
768 770 0.037326 GACATGTGGAAGCTCGACCA 60.037 55.000 1.15 3.60 0.00 4.02
769 771 0.247736 AGACATGTGGAAGCTCGACC 59.752 55.000 1.15 0.00 0.00 4.79
770 772 2.164624 ACTAGACATGTGGAAGCTCGAC 59.835 50.000 1.15 0.00 0.00 4.20
771 773 2.423892 GACTAGACATGTGGAAGCTCGA 59.576 50.000 1.15 0.00 0.00 4.04
772 774 2.792890 CGACTAGACATGTGGAAGCTCG 60.793 54.545 1.15 6.25 0.00 5.03
773 775 2.423892 TCGACTAGACATGTGGAAGCTC 59.576 50.000 1.15 0.00 0.00 4.09
774 776 2.425312 CTCGACTAGACATGTGGAAGCT 59.575 50.000 1.15 0.00 0.00 3.74
775 777 2.803451 CTCGACTAGACATGTGGAAGC 58.197 52.381 1.15 0.00 0.00 3.86
776 778 2.164422 TGCTCGACTAGACATGTGGAAG 59.836 50.000 1.15 0.00 0.00 3.46
777 779 2.164422 CTGCTCGACTAGACATGTGGAA 59.836 50.000 1.15 0.00 0.00 3.53
778 780 1.745653 CTGCTCGACTAGACATGTGGA 59.254 52.381 1.15 0.00 0.00 4.02
779 781 1.745653 TCTGCTCGACTAGACATGTGG 59.254 52.381 1.15 0.00 0.00 4.17
780 782 3.175152 GTTCTGCTCGACTAGACATGTG 58.825 50.000 1.15 0.00 0.00 3.21
781 783 2.820197 TGTTCTGCTCGACTAGACATGT 59.180 45.455 0.00 0.00 0.00 3.21
782 784 3.433709 CTGTTCTGCTCGACTAGACATG 58.566 50.000 0.00 0.00 0.00 3.21
783 785 2.425312 CCTGTTCTGCTCGACTAGACAT 59.575 50.000 0.00 0.00 0.00 3.06
784 786 1.813178 CCTGTTCTGCTCGACTAGACA 59.187 52.381 0.00 0.00 0.00 3.41
785 787 1.813786 ACCTGTTCTGCTCGACTAGAC 59.186 52.381 0.00 0.00 0.00 2.59
786 788 1.813178 CACCTGTTCTGCTCGACTAGA 59.187 52.381 0.00 0.00 0.00 2.43
787 789 1.813178 TCACCTGTTCTGCTCGACTAG 59.187 52.381 0.00 0.00 0.00 2.57
788 790 1.905637 TCACCTGTTCTGCTCGACTA 58.094 50.000 0.00 0.00 0.00 2.59
789 791 1.067283 CATCACCTGTTCTGCTCGACT 60.067 52.381 0.00 0.00 0.00 4.18
790 792 1.354040 CATCACCTGTTCTGCTCGAC 58.646 55.000 0.00 0.00 0.00 4.20
791 793 0.390340 GCATCACCTGTTCTGCTCGA 60.390 55.000 0.00 0.00 0.00 4.04
792 794 0.390866 AGCATCACCTGTTCTGCTCG 60.391 55.000 0.00 0.00 40.85 5.03
793 795 3.547567 AGCATCACCTGTTCTGCTC 57.452 52.632 0.00 0.00 40.85 4.26
795 797 0.390340 TCGAGCATCACCTGTTCTGC 60.390 55.000 0.00 0.00 33.24 4.26
796 798 1.337167 TGTCGAGCATCACCTGTTCTG 60.337 52.381 0.00 0.00 33.24 3.02
797 799 0.969149 TGTCGAGCATCACCTGTTCT 59.031 50.000 0.00 0.00 33.24 3.01
798 800 1.071605 GTGTCGAGCATCACCTGTTC 58.928 55.000 0.00 0.00 33.17 3.18
799 801 3.217242 GTGTCGAGCATCACCTGTT 57.783 52.632 0.00 0.00 33.17 3.16
800 802 4.996976 GTGTCGAGCATCACCTGT 57.003 55.556 0.00 0.00 33.17 4.00
804 806 1.357258 CTGCTGGTGTCGAGCATCAC 61.357 60.000 6.88 0.00 45.27 3.06
805 807 1.079612 CTGCTGGTGTCGAGCATCA 60.080 57.895 6.88 0.00 45.27 3.07
806 808 1.812922 CCTGCTGGTGTCGAGCATC 60.813 63.158 6.88 0.00 45.27 3.91
807 809 2.267006 CCTGCTGGTGTCGAGCAT 59.733 61.111 6.88 0.00 45.27 3.79
808 810 3.233980 ACCTGCTGGTGTCGAGCA 61.234 61.111 15.36 6.32 46.51 4.26
821 823 1.091771 CACTGGGAGCGCAATACCTG 61.092 60.000 11.47 6.72 0.00 4.00
822 824 1.221840 CACTGGGAGCGCAATACCT 59.778 57.895 11.47 0.00 0.00 3.08
823 825 2.472909 GCACTGGGAGCGCAATACC 61.473 63.158 11.47 0.00 0.00 2.73
824 826 3.102097 GCACTGGGAGCGCAATAC 58.898 61.111 11.47 0.00 0.00 1.89
831 833 3.426568 GCTCAACGCACTGGGAGC 61.427 66.667 0.00 0.00 44.97 4.70
832 834 1.302033 AAGCTCAACGCACTGGGAG 60.302 57.895 0.00 0.00 42.61 4.30
833 835 1.597854 CAAGCTCAACGCACTGGGA 60.598 57.895 0.00 0.00 42.61 4.37
834 836 2.620112 CCAAGCTCAACGCACTGGG 61.620 63.158 0.00 0.00 42.61 4.45
869 876 2.677337 GCAAAGGAAGATGAGCTGTCTC 59.323 50.000 0.00 0.00 39.78 3.36
893 900 6.073765 GCGTAAACAAAGAGAGATGTTTCTGA 60.074 38.462 7.11 0.00 44.16 3.27
896 903 6.074005 CAGCGTAAACAAAGAGAGATGTTTC 58.926 40.000 7.11 0.71 44.16 2.78
909 916 2.670251 CCGGGGCAGCGTAAACAA 60.670 61.111 0.00 0.00 0.00 2.83
1475 1487 1.070601 GCAGGAATGTTTGCCCAACTT 59.929 47.619 0.00 0.00 36.21 2.66
1481 1493 1.079612 GGCTGCAGGAATGTTTGCC 60.080 57.895 17.12 3.67 39.54 4.52
1483 1495 0.597568 TTCGGCTGCAGGAATGTTTG 59.402 50.000 17.12 0.00 0.00 2.93
1540 1552 6.017400 AGCACACTACTGAATTGGATTTTG 57.983 37.500 0.00 0.00 0.00 2.44
1541 1553 7.944729 ATAGCACACTACTGAATTGGATTTT 57.055 32.000 0.00 0.00 0.00 1.82
1573 1586 2.437200 CATGGTGATGCACGGTTTTT 57.563 45.000 0.00 0.00 34.83 1.94
1619 1633 3.063997 CGTCAAAGTATCCAAGATGGCAC 59.936 47.826 0.00 0.00 37.47 5.01
1622 1636 4.568359 CACTCGTCAAAGTATCCAAGATGG 59.432 45.833 0.00 0.00 39.43 3.51
1623 1637 5.171476 ACACTCGTCAAAGTATCCAAGATG 58.829 41.667 0.00 0.00 0.00 2.90
1626 1640 6.128634 GGTTTACACTCGTCAAAGTATCCAAG 60.129 42.308 0.00 0.00 0.00 3.61
1627 1641 5.697633 GGTTTACACTCGTCAAAGTATCCAA 59.302 40.000 0.00 0.00 0.00 3.53
1628 1642 5.011329 AGGTTTACACTCGTCAAAGTATCCA 59.989 40.000 0.00 0.00 0.00 3.41
1629 1643 5.476614 AGGTTTACACTCGTCAAAGTATCC 58.523 41.667 0.00 0.00 0.00 2.59
1630 1644 7.596248 TGTTAGGTTTACACTCGTCAAAGTATC 59.404 37.037 0.00 0.00 0.00 2.24
1631 1645 7.383300 GTGTTAGGTTTACACTCGTCAAAGTAT 59.617 37.037 0.00 0.00 41.99 2.12
1632 1646 6.697019 GTGTTAGGTTTACACTCGTCAAAGTA 59.303 38.462 0.00 0.00 41.99 2.24
1633 1647 5.521372 GTGTTAGGTTTACACTCGTCAAAGT 59.479 40.000 0.00 0.00 41.99 2.66
1634 1648 5.970879 GTGTTAGGTTTACACTCGTCAAAG 58.029 41.667 0.00 0.00 41.99 2.77
1635 1649 5.971895 GTGTTAGGTTTACACTCGTCAAA 57.028 39.130 0.00 0.00 41.99 2.69
1643 1657 6.793680 GCAATCGTAAAGTGTTAGGTTTACAC 59.206 38.462 0.00 0.00 44.81 2.90
1644 1658 6.482641 TGCAATCGTAAAGTGTTAGGTTTACA 59.517 34.615 5.96 0.00 38.51 2.41
1645 1659 6.793680 GTGCAATCGTAAAGTGTTAGGTTTAC 59.206 38.462 0.00 0.00 36.28 2.01
1646 1660 6.707161 AGTGCAATCGTAAAGTGTTAGGTTTA 59.293 34.615 0.00 0.00 0.00 2.01
1647 1661 5.529800 AGTGCAATCGTAAAGTGTTAGGTTT 59.470 36.000 0.00 0.00 0.00 3.27
1648 1662 5.049680 CAGTGCAATCGTAAAGTGTTAGGTT 60.050 40.000 0.00 0.00 0.00 3.50
1653 1674 5.689383 ATTCAGTGCAATCGTAAAGTGTT 57.311 34.783 0.00 0.00 0.00 3.32
1668 1689 0.179240 GCGCGTGTGAGAATTCAGTG 60.179 55.000 8.43 0.07 32.98 3.66
1672 1693 2.395690 CCGCGCGTGTGAGAATTC 59.604 61.111 29.95 0.00 0.00 2.17
1674 1695 4.373116 ACCCGCGCGTGTGAGAAT 62.373 61.111 29.95 0.00 0.00 2.40
1713 1734 1.837439 TGGTTGAGCAATAGATCCGGT 59.163 47.619 0.00 0.00 0.00 5.28
1734 1755 1.377202 GAGCCCACGAAGCCAATCA 60.377 57.895 0.00 0.00 0.00 2.57
1770 1791 3.198853 AGCCAGGACCATAGAGAAGAAAC 59.801 47.826 0.00 0.00 0.00 2.78
1815 1836 0.033781 GCTTGGGCATGCTTTTGTCA 59.966 50.000 18.92 4.19 38.54 3.58
1929 1950 1.472552 CCTGGAACGACAACAGACACA 60.473 52.381 0.00 0.00 34.21 3.72
1930 1951 1.217882 CCTGGAACGACAACAGACAC 58.782 55.000 0.00 0.00 34.21 3.67
2103 2124 3.717404 CGTTCAAGCACAACGTTAAGAAC 59.283 43.478 0.00 8.25 41.39 3.01
2112 2133 3.917985 AGTTGTTTTCGTTCAAGCACAAC 59.082 39.130 5.09 5.09 38.83 3.32
2156 2179 5.186256 TGAACCCTGCAATACCAGAATAA 57.814 39.130 0.00 0.00 34.77 1.40
2157 2180 4.853468 TGAACCCTGCAATACCAGAATA 57.147 40.909 0.00 0.00 34.77 1.75
2255 2279 7.337942 CACTAGAGTGGGATTAGAAAAATGCTT 59.662 37.037 0.00 0.00 42.10 3.91
2311 2335 5.857822 ACGGCTGTTTAGATAAAGTGAAC 57.142 39.130 0.00 0.00 0.00 3.18
2489 2514 6.536582 ACGGTAATCATCAGAGATTTTGAGTG 59.463 38.462 0.00 0.00 38.97 3.51
2502 2527 1.483316 CGCGCTTACGGTAATCATCA 58.517 50.000 5.56 0.00 40.57 3.07
2512 2537 4.891727 ATGCTCCCCGCGCTTACG 62.892 66.667 5.56 0.00 43.27 3.18
2524 2550 5.402398 AGCCGATCTTTTGTTAAAATGCTC 58.598 37.500 0.00 0.00 0.00 4.26
2525 2551 5.391312 AGCCGATCTTTTGTTAAAATGCT 57.609 34.783 0.00 0.00 0.00 3.79
2636 2662 2.342650 CCACCACCAGAATTGCCCG 61.343 63.158 0.00 0.00 0.00 6.13
2728 2754 7.642978 GCAACATGCTCATAGATGTTTAGAAAG 59.357 37.037 0.00 0.00 40.12 2.62
2782 2808 5.248640 AGGTCACTGAACAAATGATACAGG 58.751 41.667 0.00 0.00 33.57 4.00
2984 3011 2.100087 GACCACGAAAAGGGAAAAAGCA 59.900 45.455 0.00 0.00 0.00 3.91
2985 3012 2.100087 TGACCACGAAAAGGGAAAAAGC 59.900 45.455 0.00 0.00 0.00 3.51
2986 3013 4.379339 TTGACCACGAAAAGGGAAAAAG 57.621 40.909 0.00 0.00 0.00 2.27
3024 3052 8.784043 GGAACAGTTTGTGATTAGTGAACTATT 58.216 33.333 0.00 0.00 0.00 1.73
3027 3055 6.357367 AGGAACAGTTTGTGATTAGTGAACT 58.643 36.000 0.00 0.00 0.00 3.01
3085 3116 3.500343 ACAAGAATTTTGGGACAGAGGG 58.500 45.455 5.68 0.00 42.39 4.30
3086 3117 4.401925 AGACAAGAATTTTGGGACAGAGG 58.598 43.478 5.68 0.00 42.39 3.69
3087 3118 6.936900 TCTAAGACAAGAATTTTGGGACAGAG 59.063 38.462 5.68 0.00 42.39 3.35
3088 3119 6.837312 TCTAAGACAAGAATTTTGGGACAGA 58.163 36.000 5.68 0.00 42.39 3.41
3089 3120 7.693969 ATCTAAGACAAGAATTTTGGGACAG 57.306 36.000 5.68 0.00 42.39 3.51
3090 3121 8.359642 CAAATCTAAGACAAGAATTTTGGGACA 58.640 33.333 5.68 0.00 28.49 4.02
3091 3122 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3092 3123 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3093 3124 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3101 3132 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
3102 3133 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
3104 3135 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
3105 3136 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
3112 3143 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
3113 3144 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
3114 3145 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
3115 3146 8.002984 TGACTTGATACATCCGTATTTAGACA 57.997 34.615 0.00 0.00 38.48 3.41
3116 3147 8.916654 CATGACTTGATACATCCGTATTTAGAC 58.083 37.037 0.00 0.00 38.48 2.59
3117 3148 8.638873 ACATGACTTGATACATCCGTATTTAGA 58.361 33.333 0.00 0.00 38.48 2.10
3118 3149 8.818141 ACATGACTTGATACATCCGTATTTAG 57.182 34.615 0.00 0.00 38.48 1.85
3119 3150 9.607988 AAACATGACTTGATACATCCGTATTTA 57.392 29.630 0.00 0.00 38.48 1.40
3120 3151 8.506168 AAACATGACTTGATACATCCGTATTT 57.494 30.769 0.00 0.00 38.48 1.40
3121 3152 8.506168 AAAACATGACTTGATACATCCGTATT 57.494 30.769 0.00 0.00 38.48 1.89
3122 3153 9.261180 CTAAAACATGACTTGATACATCCGTAT 57.739 33.333 0.00 0.00 41.16 3.06
3123 3154 8.255206 ACTAAAACATGACTTGATACATCCGTA 58.745 33.333 0.00 0.00 0.00 4.02
3124 3155 7.103641 ACTAAAACATGACTTGATACATCCGT 58.896 34.615 0.00 0.00 0.00 4.69
3125 3156 7.539712 ACTAAAACATGACTTGATACATCCG 57.460 36.000 0.00 0.00 0.00 4.18
3126 3157 9.601217 AGTACTAAAACATGACTTGATACATCC 57.399 33.333 0.00 0.00 0.00 3.51
3147 3178 9.993454 TGTCTAGATACGAATGTATGTAGTACT 57.007 33.333 15.14 0.00 46.93 2.73
3157 3188 9.953697 GTCTTAGATTTGTCTAGATACGAATGT 57.046 33.333 0.00 0.00 34.30 2.71
3158 3189 9.952188 TGTCTTAGATTTGTCTAGATACGAATG 57.048 33.333 0.00 0.00 34.30 2.67
3161 3192 9.392259 TCTTGTCTTAGATTTGTCTAGATACGA 57.608 33.333 0.00 0.00 0.00 3.43
3169 3200 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3170 3201 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3171 3202 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3172 3203 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3173 3204 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3174 3205 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3175 3206 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3176 3207 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3177 3208 4.379499 GCCGTCCCAAAATTCTTGTCTTAG 60.379 45.833 0.00 0.00 0.00 2.18
3178 3209 3.504520 GCCGTCCCAAAATTCTTGTCTTA 59.495 43.478 0.00 0.00 0.00 2.10
3179 3210 2.296190 GCCGTCCCAAAATTCTTGTCTT 59.704 45.455 0.00 0.00 0.00 3.01
3180 3211 1.886542 GCCGTCCCAAAATTCTTGTCT 59.113 47.619 0.00 0.00 0.00 3.41
3181 3212 1.611491 TGCCGTCCCAAAATTCTTGTC 59.389 47.619 0.00 0.00 0.00 3.18
3182 3213 1.613437 CTGCCGTCCCAAAATTCTTGT 59.387 47.619 0.00 0.00 0.00 3.16
3183 3214 1.067635 CCTGCCGTCCCAAAATTCTTG 60.068 52.381 0.00 0.00 0.00 3.02
3184 3215 1.203001 TCCTGCCGTCCCAAAATTCTT 60.203 47.619 0.00 0.00 0.00 2.52
3185 3216 0.404040 TCCTGCCGTCCCAAAATTCT 59.596 50.000 0.00 0.00 0.00 2.40
3186 3217 0.811281 CTCCTGCCGTCCCAAAATTC 59.189 55.000 0.00 0.00 0.00 2.17
3187 3218 0.112412 ACTCCTGCCGTCCCAAAATT 59.888 50.000 0.00 0.00 0.00 1.82
3188 3219 0.988832 TACTCCTGCCGTCCCAAAAT 59.011 50.000 0.00 0.00 0.00 1.82
3189 3220 0.035739 GTACTCCTGCCGTCCCAAAA 59.964 55.000 0.00 0.00 0.00 2.44
3190 3221 0.834687 AGTACTCCTGCCGTCCCAAA 60.835 55.000 0.00 0.00 0.00 3.28
3191 3222 1.229082 AGTACTCCTGCCGTCCCAA 60.229 57.895 0.00 0.00 0.00 4.12
3192 3223 1.982395 CAGTACTCCTGCCGTCCCA 60.982 63.158 0.00 0.00 33.59 4.37
3193 3224 1.668101 CTCAGTACTCCTGCCGTCCC 61.668 65.000 0.00 0.00 41.25 4.46
3194 3225 1.810532 CTCAGTACTCCTGCCGTCC 59.189 63.158 0.00 0.00 41.25 4.79
3195 3226 1.139947 GCTCAGTACTCCTGCCGTC 59.860 63.158 0.00 0.00 41.25 4.79
3196 3227 0.034380 TAGCTCAGTACTCCTGCCGT 60.034 55.000 0.00 0.00 41.25 5.68
3197 3228 1.000827 CATAGCTCAGTACTCCTGCCG 60.001 57.143 0.00 0.00 41.25 5.69
3198 3229 1.270041 GCATAGCTCAGTACTCCTGCC 60.270 57.143 0.00 0.00 41.25 4.85
3199 3230 1.686052 AGCATAGCTCAGTACTCCTGC 59.314 52.381 0.00 0.00 41.25 4.85
3200 3231 2.954989 TCAGCATAGCTCAGTACTCCTG 59.045 50.000 0.00 0.00 42.97 3.86
3201 3232 3.221771 CTCAGCATAGCTCAGTACTCCT 58.778 50.000 0.00 0.00 36.40 3.69
3202 3233 2.955660 ACTCAGCATAGCTCAGTACTCC 59.044 50.000 0.00 0.00 38.44 3.85
3203 3234 5.060506 TCTACTCAGCATAGCTCAGTACTC 58.939 45.833 0.00 0.00 38.44 2.59
3204 3235 5.042463 TCTACTCAGCATAGCTCAGTACT 57.958 43.478 0.00 0.00 38.44 2.73
3205 3236 5.759506 TTCTACTCAGCATAGCTCAGTAC 57.240 43.478 0.00 0.00 38.44 2.73
3206 3237 6.405953 GGTTTTCTACTCAGCATAGCTCAGTA 60.406 42.308 2.85 2.85 38.44 2.74
3207 3238 5.415221 GTTTTCTACTCAGCATAGCTCAGT 58.585 41.667 0.44 0.44 43.55 3.41
3208 3239 4.808364 GGTTTTCTACTCAGCATAGCTCAG 59.192 45.833 0.00 0.00 36.40 3.35
3209 3240 4.222810 TGGTTTTCTACTCAGCATAGCTCA 59.777 41.667 0.00 0.00 36.40 4.26
3222 3253 8.957466 AGGCTTCACTAATAAATGGTTTTCTAC 58.043 33.333 0.00 0.00 0.00 2.59
3250 3281 0.472734 AGCCAACAGAGTCTGGACCT 60.473 55.000 23.79 11.23 35.51 3.85
3254 3285 2.260844 TGAAAGCCAACAGAGTCTGG 57.739 50.000 23.79 8.76 35.51 3.86
3430 3462 5.235831 AGAAGTGGTAGTTTTACAAGCGTTC 59.764 40.000 0.00 0.00 0.00 3.95
3655 3731 4.095410 TGTGCATGAAAAATTAGCTCCG 57.905 40.909 0.00 0.00 0.00 4.63
3657 3733 7.035004 TGGTAATGTGCATGAAAAATTAGCTC 58.965 34.615 15.54 0.00 34.12 4.09
3658 3734 6.934056 TGGTAATGTGCATGAAAAATTAGCT 58.066 32.000 15.54 0.00 34.12 3.32
3720 3796 8.260818 AGTGAATTAGCAACTGTGTAGTGATAT 58.739 33.333 0.00 0.00 37.19 1.63
3783 3860 9.346725 GTTGATTTTTCCTGATACATTCTTGAC 57.653 33.333 0.00 0.00 0.00 3.18
3844 3921 9.251792 GTATTTGAAAAAGGAAACGGTAACATT 57.748 29.630 0.00 0.00 0.00 2.71
3869 3946 8.250143 ACAATTTCTATGAGGAAACCAAAAGT 57.750 30.769 0.00 0.00 37.91 2.66
3870 3947 8.359642 TGACAATTTCTATGAGGAAACCAAAAG 58.640 33.333 0.00 0.00 37.91 2.27
3871 3948 8.243961 TGACAATTTCTATGAGGAAACCAAAA 57.756 30.769 0.00 0.00 37.91 2.44


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

AutoCloner maintained by Alex Coulton.