Multiple sequence alignment - TraesCS3B01G330800

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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 TraesCS3B01G330800 chr3B 100.000 6054 0 0 1 6054 535528274 535534327 0.000000e+00 11180.0
1 TraesCS3B01G330800 chr3B 96.291 728 25 2 5326 6053 473088424 473087699 0.000000e+00 1194.0
2 TraesCS3B01G330800 chr3B 96.143 726 27 1 5328 6053 429111514 429110790 0.000000e+00 1184.0
3 TraesCS3B01G330800 chr3B 95.954 519 18 3 1 517 829474137 829473620 0.000000e+00 839.0
4 TraesCS3B01G330800 chr3B 95.385 520 20 4 1 517 48018374 48018892 0.000000e+00 824.0
5 TraesCS3B01G330800 chr3B 94.808 520 24 3 1 517 47675011 47675530 0.000000e+00 808.0
6 TraesCS3B01G330800 chr3B 94.808 520 24 3 1 517 783294805 783294286 0.000000e+00 808.0
7 TraesCS3B01G330800 chr3B 94.423 520 27 2 1 519 14988523 14988005 0.000000e+00 798.0
8 TraesCS3B01G330800 chr3B 94.563 515 24 4 1 513 577492980 577492468 0.000000e+00 793.0
9 TraesCS3B01G330800 chr3D 91.326 4923 220 97 517 5331 409928966 409933789 0.000000e+00 6534.0
10 TraesCS3B01G330800 chr3A 92.169 1724 87 27 2549 4256 541638142 541636451 0.000000e+00 2392.0
11 TraesCS3B01G330800 chr3A 88.471 1995 92 51 608 2501 541640097 541638140 0.000000e+00 2283.0
12 TraesCS3B01G330800 chr3A 94.062 640 20 7 4278 4905 541636102 541635469 0.000000e+00 955.0
13 TraesCS3B01G330800 chr3A 86.395 147 9 6 519 657 541640244 541640101 3.780000e-32 150.0
14 TraesCS3B01G330800 chr3A 91.250 80 5 2 5252 5331 541635327 541635250 2.310000e-19 108.0
15 TraesCS3B01G330800 chr7B 96.699 727 22 2 5328 6053 376753769 376753044 0.000000e+00 1208.0
16 TraesCS3B01G330800 chr7B 96.443 731 25 1 5323 6053 124552209 124552938 0.000000e+00 1205.0
17 TraesCS3B01G330800 chr7B 96.016 728 25 2 5326 6053 638994933 638995656 0.000000e+00 1181.0
18 TraesCS3B01G330800 chr7B 95.424 743 27 4 5311 6053 461567771 461568506 0.000000e+00 1177.0
19 TraesCS3B01G330800 chr5B 96.552 725 24 1 5329 6053 307596098 307596821 0.000000e+00 1199.0
20 TraesCS3B01G330800 chr5B 96.154 728 27 1 5326 6053 349052860 349052134 0.000000e+00 1188.0
21 TraesCS3B01G330800 chr5B 89.362 47 5 0 5012 5058 78228559 78228605 6.550000e-05 60.2
22 TraesCS3B01G330800 chr6B 96.276 725 26 1 5329 6053 279479489 279478766 0.000000e+00 1188.0
23 TraesCS3B01G330800 chrUn 94.760 687 32 4 1603 2289 309504749 309504067 0.000000e+00 1066.0
24 TraesCS3B01G330800 chrUn 94.107 577 31 3 1713 2289 269283203 269283776 0.000000e+00 874.0
25 TraesCS3B01G330800 chrUn 93.761 577 33 3 1713 2289 250117101 250117674 0.000000e+00 863.0
26 TraesCS3B01G330800 chrUn 93.064 519 33 3 1771 2289 310483238 310482723 0.000000e+00 756.0
27 TraesCS3B01G330800 chrUn 93.217 516 32 3 1771 2286 310483339 310483851 0.000000e+00 756.0
28 TraesCS3B01G330800 chrUn 89.802 353 20 8 2555 2907 324205260 324205596 7.200000e-119 438.0
29 TraesCS3B01G330800 chrUn 89.802 353 20 8 2555 2907 366320272 366319936 7.200000e-119 438.0
30 TraesCS3B01G330800 chrUn 89.136 359 23 8 2549 2907 250121242 250121584 3.350000e-117 433.0
31 TraesCS3B01G330800 chrUn 89.136 359 23 7 2549 2907 267564429 267564771 3.350000e-117 433.0
32 TraesCS3B01G330800 chrUn 89.136 359 23 7 2549 2907 269286923 269287265 3.350000e-117 433.0
33 TraesCS3B01G330800 chrUn 89.136 359 23 8 2549 2907 318576172 318575830 3.350000e-117 433.0
34 TraesCS3B01G330800 chrUn 89.136 359 23 8 2549 2907 333585595 333585253 3.350000e-117 433.0
35 TraesCS3B01G330800 chrUn 91.146 192 17 0 2310 2501 324205065 324205256 1.670000e-65 261.0
36 TraesCS3B01G330800 chrUn 91.146 192 17 0 2310 2501 366320467 366320276 1.670000e-65 261.0
37 TraesCS3B01G330800 chrUn 91.146 192 16 1 2310 2501 267564241 267564431 6.020000e-65 259.0
38 TraesCS3B01G330800 chrUn 91.146 192 16 1 2310 2501 269286735 269286925 6.020000e-65 259.0
39 TraesCS3B01G330800 chrUn 90.104 192 19 0 2310 2501 250121053 250121244 3.620000e-62 250.0
40 TraesCS3B01G330800 chrUn 96.610 118 4 0 1603 1720 330015843 330015960 4.790000e-46 196.0
41 TraesCS3B01G330800 chrUn 96.610 118 4 0 1603 1720 333421898 333421781 4.790000e-46 196.0
42 TraesCS3B01G330800 chrUn 96.610 118 4 0 1603 1720 360360402 360360285 4.790000e-46 196.0
43 TraesCS3B01G330800 chrUn 96.610 118 4 0 1603 1720 360789875 360789758 4.790000e-46 196.0
44 TraesCS3B01G330800 chrUn 96.610 118 4 0 1603 1720 376430039 376430156 4.790000e-46 196.0
45 TraesCS3B01G330800 chrUn 83.495 103 11 5 5018 5115 75090642 75090541 2.320000e-14 91.6
46 TraesCS3B01G330800 chr1D 94.454 577 28 4 1713 2289 17288383 17287811 0.000000e+00 885.0
47 TraesCS3B01G330800 chr1D 94.281 577 30 3 1713 2289 17373406 17372833 0.000000e+00 880.0
48 TraesCS3B01G330800 chr1D 93.588 577 34 3 1713 2289 17300072 17299499 0.000000e+00 857.0
49 TraesCS3B01G330800 chr1D 89.802 353 20 8 2555 2907 17284231 17283895 7.200000e-119 438.0
50 TraesCS3B01G330800 chr1D 89.136 359 23 8 2549 2907 17295931 17295589 3.350000e-117 433.0
51 TraesCS3B01G330800 chr1D 89.136 359 23 7 2549 2907 17369686 17369344 3.350000e-117 433.0
52 TraesCS3B01G330800 chr1D 96.407 167 6 0 1603 1769 17411655 17411489 5.980000e-70 276.0
53 TraesCS3B01G330800 chr1D 91.146 192 17 0 2310 2501 17284426 17284235 1.670000e-65 261.0
54 TraesCS3B01G330800 chr1D 91.146 192 16 1 2310 2501 17369874 17369684 6.020000e-65 259.0
55 TraesCS3B01G330800 chr1B 95.577 520 19 4 1 516 653673615 653674134 0.000000e+00 830.0
56 TraesCS3B01G330800 chr1B 94.818 521 24 3 1 519 643907054 643906535 0.000000e+00 809.0
57 TraesCS3B01G330800 chr1B 79.487 195 25 10 4928 5112 443004555 443004366 2.290000e-24 124.0
58 TraesCS3B01G330800 chr2B 94.646 523 21 4 1 520 93076185 93075667 0.000000e+00 804.0
59 TraesCS3B01G330800 chr4B 82.684 231 27 8 4891 5112 657478939 657478713 6.190000e-45 193.0
60 TraesCS3B01G330800 chr6A 81.429 140 13 7 4984 5112 60056090 60056227 1.070000e-17 102.0
61 TraesCS3B01G330800 chr5D 89.362 47 5 0 5012 5058 74115025 74114979 6.550000e-05 60.2
62 TraesCS3B01G330800 chr5A 89.583 48 3 2 5012 5058 69128476 69128430 6.550000e-05 60.2
63 TraesCS3B01G330800 chr1A 100.000 28 0 0 5010 5037 539319386 539319413 1.100000e-02 52.8


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 TraesCS3B01G330800 chr3B 535528274 535534327 6053 False 11180.000000 11180 100.000000 1 6054 1 chr3B.!!$F3 6053
1 TraesCS3B01G330800 chr3B 473087699 473088424 725 True 1194.000000 1194 96.291000 5326 6053 1 chr3B.!!$R3 727
2 TraesCS3B01G330800 chr3B 429110790 429111514 724 True 1184.000000 1184 96.143000 5328 6053 1 chr3B.!!$R2 725
3 TraesCS3B01G330800 chr3B 829473620 829474137 517 True 839.000000 839 95.954000 1 517 1 chr3B.!!$R6 516
4 TraesCS3B01G330800 chr3B 48018374 48018892 518 False 824.000000 824 95.385000 1 517 1 chr3B.!!$F2 516
5 TraesCS3B01G330800 chr3B 47675011 47675530 519 False 808.000000 808 94.808000 1 517 1 chr3B.!!$F1 516
6 TraesCS3B01G330800 chr3B 783294286 783294805 519 True 808.000000 808 94.808000 1 517 1 chr3B.!!$R5 516
7 TraesCS3B01G330800 chr3B 14988005 14988523 518 True 798.000000 798 94.423000 1 519 1 chr3B.!!$R1 518
8 TraesCS3B01G330800 chr3B 577492468 577492980 512 True 793.000000 793 94.563000 1 513 1 chr3B.!!$R4 512
9 TraesCS3B01G330800 chr3D 409928966 409933789 4823 False 6534.000000 6534 91.326000 517 5331 1 chr3D.!!$F1 4814
10 TraesCS3B01G330800 chr3A 541635250 541640244 4994 True 1177.600000 2392 90.469400 519 5331 5 chr3A.!!$R1 4812
11 TraesCS3B01G330800 chr7B 376753044 376753769 725 True 1208.000000 1208 96.699000 5328 6053 1 chr7B.!!$R1 725
12 TraesCS3B01G330800 chr7B 124552209 124552938 729 False 1205.000000 1205 96.443000 5323 6053 1 chr7B.!!$F1 730
13 TraesCS3B01G330800 chr7B 638994933 638995656 723 False 1181.000000 1181 96.016000 5326 6053 1 chr7B.!!$F3 727
14 TraesCS3B01G330800 chr7B 461567771 461568506 735 False 1177.000000 1177 95.424000 5311 6053 1 chr7B.!!$F2 742
15 TraesCS3B01G330800 chr5B 307596098 307596821 723 False 1199.000000 1199 96.552000 5329 6053 1 chr5B.!!$F2 724
16 TraesCS3B01G330800 chr5B 349052134 349052860 726 True 1188.000000 1188 96.154000 5326 6053 1 chr5B.!!$R1 727
17 TraesCS3B01G330800 chr6B 279478766 279479489 723 True 1188.000000 1188 96.276000 5329 6053 1 chr6B.!!$R1 724
18 TraesCS3B01G330800 chrUn 309504067 309504749 682 True 1066.000000 1066 94.760000 1603 2289 1 chrUn.!!$R2 686
19 TraesCS3B01G330800 chrUn 310482723 310483238 515 True 756.000000 756 93.064000 1771 2289 1 chrUn.!!$R3 518
20 TraesCS3B01G330800 chrUn 310483339 310483851 512 False 756.000000 756 93.217000 1771 2286 1 chrUn.!!$F1 515
21 TraesCS3B01G330800 chrUn 269283203 269287265 4062 False 522.000000 874 91.463000 1713 2907 3 chrUn.!!$F6 1194
22 TraesCS3B01G330800 chrUn 250117101 250121584 4483 False 515.333333 863 91.000333 1713 2907 3 chrUn.!!$F4 1194
23 TraesCS3B01G330800 chrUn 324205065 324205596 531 False 349.500000 438 90.474000 2310 2907 2 chrUn.!!$F7 597
24 TraesCS3B01G330800 chrUn 366319936 366320467 531 True 349.500000 438 90.474000 2310 2907 2 chrUn.!!$R9 597
25 TraesCS3B01G330800 chrUn 267564241 267564771 530 False 346.000000 433 90.141000 2310 2907 2 chrUn.!!$F5 597
26 TraesCS3B01G330800 chr1D 17295589 17300072 4483 True 645.000000 857 91.362000 1713 2907 2 chr1D.!!$R3 1194
27 TraesCS3B01G330800 chr1D 17283895 17288383 4488 True 528.000000 885 91.800667 1713 2907 3 chr1D.!!$R2 1194
28 TraesCS3B01G330800 chr1D 17369344 17373406 4062 True 524.000000 880 91.521000 1713 2907 3 chr1D.!!$R4 1194
29 TraesCS3B01G330800 chr1B 653673615 653674134 519 False 830.000000 830 95.577000 1 516 1 chr1B.!!$F1 515
30 TraesCS3B01G330800 chr1B 643906535 643907054 519 True 809.000000 809 94.818000 1 519 1 chr1B.!!$R2 518
31 TraesCS3B01G330800 chr2B 93075667 93076185 518 True 804.000000 804 94.646000 1 520 1 chr2B.!!$R1 519

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
836 922 0.260816 TGCGGATGTCCTAGGTAGGT 59.739 55.0 9.08 0.0 44.02 3.08 F
1595 1745 0.038159 GGGTGAGTGACTCCGACAAG 60.038 60.0 10.52 0.0 33.42 3.16 F
1597 1747 0.038159 GTGAGTGACTCCGACAAGGG 60.038 60.0 10.52 0.0 41.52 3.95 F
1601 1751 0.108138 GTGACTCCGACAAGGGGATG 60.108 60.0 0.00 0.0 46.06 3.51 F
1829 1997 0.390998 TCTTGATTCGCATCGCACCA 60.391 50.0 0.00 0.0 31.08 4.17 F
3489 7043 0.681733 TATCATCTTCGAGCCCTGGC 59.318 55.0 0.00 0.0 42.33 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2691 6241 0.038166 TAGCAGCAAAGACTTGGGGG 59.962 55.000 0.00 0.0 32.76 5.40 R
2724 6274 0.038526 AACTTCCTAGCACGACACGG 60.039 55.000 0.00 0.0 0.00 4.94 R
2954 6504 0.463295 ACCATGGCGCAGAAGAGATG 60.463 55.000 13.04 0.0 0.00 2.90 R
3246 6798 1.326548 GACACCATACCGAACGATTGC 59.673 52.381 0.00 0.0 0.00 3.56 R
3587 7141 1.753073 CCACAAAGGAGGATGCCAATC 59.247 52.381 0.00 0.0 41.22 2.67 R
5436 9386 0.472471 TTCCACGCCAAGGAAAGTCT 59.528 50.000 0.00 0.0 41.94 3.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.215382 CAGGACTCCATCGCGTTGA 59.785 57.895 18.44 6.76 0.00 3.18
238 240 1.229209 AAGGAGGAGAAGGCCGACA 60.229 57.895 0.00 0.00 0.00 4.35
564 580 2.589014 GCGTGCCAAGAAAGATCTTTG 58.411 47.619 25.12 11.70 43.43 2.77
572 588 3.425162 AGAAAGATCTTTGGGTCGCTT 57.575 42.857 25.12 0.00 32.11 4.68
583 599 4.285851 GTCGCTTCTGGACCTTGG 57.714 61.111 0.00 0.00 0.00 3.61
662 739 5.981017 TGGCACGAAAGTATTTACCGCCA 62.981 47.826 0.00 0.00 46.59 5.69
664 741 2.349590 ACGAAAGTATTTACCGCCACC 58.650 47.619 0.00 0.00 46.88 4.61
678 755 2.124693 CCACCACCACCTTTTGCGT 61.125 57.895 0.00 0.00 0.00 5.24
731 808 3.345414 AGTCTGGTCGTCAAGTAGTAGG 58.655 50.000 0.00 0.00 0.00 3.18
732 809 2.089980 TCTGGTCGTCAAGTAGTAGGC 58.910 52.381 0.00 0.00 0.00 3.93
770 856 2.562738 GACATGGTTCAAAGGAAAGGGG 59.437 50.000 0.00 0.00 34.13 4.79
836 922 0.260816 TGCGGATGTCCTAGGTAGGT 59.739 55.000 9.08 0.00 44.02 3.08
857 943 3.812544 TAGGAGCGGCCGGTAGGA 61.813 66.667 32.54 15.33 43.43 2.94
870 956 3.734902 GCCGGTAGGAAAATGAAATGCAG 60.735 47.826 1.90 0.00 41.02 4.41
874 960 2.950433 AGGAAAATGAAATGCAGTGCG 58.050 42.857 11.20 0.00 0.00 5.34
929 1020 3.003763 GGCCAGTTCTCCGGGAGT 61.004 66.667 22.88 1.63 0.00 3.85
961 1066 2.573915 GGAGGAGGGAAGAAGAACACAT 59.426 50.000 0.00 0.00 0.00 3.21
962 1067 3.009584 GGAGGAGGGAAGAAGAACACATT 59.990 47.826 0.00 0.00 0.00 2.71
966 1071 4.505742 GGAGGGAAGAAGAACACATTCACT 60.506 45.833 0.00 0.00 38.10 3.41
1000 1107 1.475280 GACCGGAAAGCATTTAACCCC 59.525 52.381 9.46 0.00 39.27 4.95
1042 1152 4.404715 GGATAAAAGGAAAAGGTTAGGGGC 59.595 45.833 0.00 0.00 0.00 5.80
1092 1222 1.594310 GAGAAAGGCTGGCGACTCT 59.406 57.895 14.09 9.29 0.00 3.24
1136 1270 1.323412 CCAGCCGCAGTATCTCTAGT 58.677 55.000 0.00 0.00 0.00 2.57
1144 1278 4.033129 CCGCAGTATCTCTAGTATCGTAGC 59.967 50.000 0.00 0.00 0.00 3.58
1145 1279 4.626172 CGCAGTATCTCTAGTATCGTAGCA 59.374 45.833 0.00 0.00 0.00 3.49
1146 1280 5.220322 CGCAGTATCTCTAGTATCGTAGCAG 60.220 48.000 0.00 0.00 0.00 4.24
1189 1323 4.760047 TTCGCCCCTCGCTTGCTC 62.760 66.667 0.00 0.00 38.27 4.26
1206 1340 1.142465 GCTCACCACCATCATCATCCT 59.858 52.381 0.00 0.00 0.00 3.24
1315 1450 0.317479 CGTCCGGTTGTCTTCTTCCT 59.683 55.000 0.00 0.00 0.00 3.36
1332 1467 3.003173 TCCGCCAGAGGACAAGGG 61.003 66.667 0.00 0.00 34.92 3.95
1406 1541 1.330655 TAAGCGAGGGAGGGAAGCAG 61.331 60.000 0.00 0.00 0.00 4.24
1585 1735 4.152248 CCTCCATGGGGTGAGTGA 57.848 61.111 11.67 0.00 34.93 3.41
1587 1737 0.911525 CCTCCATGGGGTGAGTGACT 60.912 60.000 11.67 0.00 34.93 3.41
1588 1738 0.539051 CTCCATGGGGTGAGTGACTC 59.461 60.000 13.02 5.47 34.93 3.36
1592 1742 2.971452 GGGGTGAGTGACTCCGAC 59.029 66.667 10.52 2.20 34.61 4.79
1593 1743 1.906824 GGGGTGAGTGACTCCGACA 60.907 63.158 10.52 0.00 34.61 4.35
1594 1744 1.469335 GGGGTGAGTGACTCCGACAA 61.469 60.000 10.52 0.00 34.61 3.18
1595 1745 0.038159 GGGTGAGTGACTCCGACAAG 60.038 60.000 10.52 0.00 33.42 3.16
1597 1747 0.038159 GTGAGTGACTCCGACAAGGG 60.038 60.000 10.52 0.00 41.52 3.95
1599 1749 0.898789 GAGTGACTCCGACAAGGGGA 60.899 60.000 0.00 0.00 46.06 4.81
1600 1750 0.252284 AGTGACTCCGACAAGGGGAT 60.252 55.000 0.00 0.00 46.06 3.85
1601 1751 0.108138 GTGACTCCGACAAGGGGATG 60.108 60.000 0.00 0.00 46.06 3.51
1611 1762 3.686016 GACAAGGGGATGCTTGTTTCTA 58.314 45.455 0.00 0.00 42.95 2.10
1613 1764 3.826729 ACAAGGGGATGCTTGTTTCTAAC 59.173 43.478 0.00 0.00 40.43 2.34
1824 1992 1.446731 GCGTTTCTTGATTCGCATCG 58.553 50.000 12.28 0.00 46.40 3.84
1826 1994 1.201910 CGTTTCTTGATTCGCATCGCA 60.202 47.619 0.00 0.00 31.08 5.10
1827 1995 2.169179 GTTTCTTGATTCGCATCGCAC 58.831 47.619 0.00 0.00 31.08 5.34
1828 1996 0.726827 TTCTTGATTCGCATCGCACC 59.273 50.000 0.00 0.00 31.08 5.01
1829 1997 0.390998 TCTTGATTCGCATCGCACCA 60.391 50.000 0.00 0.00 31.08 4.17
1873 2041 2.423185 TCACAAGTTTCAGTGCCAACAG 59.577 45.455 7.52 3.22 35.76 3.16
1887 2055 2.146342 CCAACAGTGTCTGATGGTGTC 58.854 52.381 14.91 0.00 45.42 3.67
2021 2189 2.758327 ACGGTCATAGGCGGCTCA 60.758 61.111 17.67 2.23 0.00 4.26
2063 2231 2.512515 GCCATCGTGCAGGACTCC 60.513 66.667 11.97 0.00 0.00 3.85
2072 2240 3.443925 CAGGACTCCTCGCTCGCA 61.444 66.667 0.00 0.00 0.00 5.10
2079 2247 2.152297 CTCCTCGCTCGCAGCCATAT 62.152 60.000 3.09 0.00 38.18 1.78
2122 2294 9.346725 GACCAATCATTCATTCACTTTTACTTC 57.653 33.333 0.00 0.00 0.00 3.01
2299 2482 4.873746 TTTCTCCAGGTCTGTCAAGTAG 57.126 45.455 0.00 0.00 0.00 2.57
2301 2484 3.845860 TCTCCAGGTCTGTCAAGTAGTT 58.154 45.455 0.00 0.00 0.00 2.24
2305 2488 5.084519 TCCAGGTCTGTCAAGTAGTTGTAT 58.915 41.667 10.08 0.00 34.98 2.29
2308 5857 7.036220 CCAGGTCTGTCAAGTAGTTGTATTAG 58.964 42.308 10.08 5.23 34.98 1.73
2405 5954 5.926542 TGTAACTTTCAGATTCTTCAGTCCG 59.073 40.000 0.00 0.00 0.00 4.79
2493 6043 1.065126 GGCCTGCTCTGTACCTGATTT 60.065 52.381 0.00 0.00 0.00 2.17
2550 6100 5.616866 GCAAACTCTGTATATGTGCGTGTTT 60.617 40.000 0.00 0.00 0.00 2.83
2691 6241 6.638468 CAGGTTTGAAAAGCAACTCTAATCAC 59.362 38.462 7.64 0.00 38.79 3.06
2694 6244 4.079253 TGAAAAGCAACTCTAATCACCCC 58.921 43.478 0.00 0.00 0.00 4.95
2695 6245 2.808906 AAGCAACTCTAATCACCCCC 57.191 50.000 0.00 0.00 0.00 5.40
2696 6246 1.668826 AGCAACTCTAATCACCCCCA 58.331 50.000 0.00 0.00 0.00 4.96
2697 6247 1.992557 AGCAACTCTAATCACCCCCAA 59.007 47.619 0.00 0.00 0.00 4.12
2698 6248 2.025887 AGCAACTCTAATCACCCCCAAG 60.026 50.000 0.00 0.00 0.00 3.61
2700 6250 3.610911 CAACTCTAATCACCCCCAAGTC 58.389 50.000 0.00 0.00 0.00 3.01
2701 6251 3.207044 ACTCTAATCACCCCCAAGTCT 57.793 47.619 0.00 0.00 0.00 3.24
2702 6252 3.532102 ACTCTAATCACCCCCAAGTCTT 58.468 45.455 0.00 0.00 0.00 3.01
2703 6253 3.916989 ACTCTAATCACCCCCAAGTCTTT 59.083 43.478 0.00 0.00 0.00 2.52
2704 6254 4.263506 ACTCTAATCACCCCCAAGTCTTTG 60.264 45.833 0.00 0.00 0.00 2.77
2705 6255 1.632589 AATCACCCCCAAGTCTTTGC 58.367 50.000 0.00 0.00 32.79 3.68
2709 6259 1.228675 CCCCCAAGTCTTTGCTGCT 60.229 57.895 0.00 0.00 32.79 4.24
2717 6267 5.335191 CCCAAGTCTTTGCTGCTAGTTAAAG 60.335 44.000 0.00 2.13 32.79 1.85
2724 6274 9.331106 GTCTTTGCTGCTAGTTAAAGTAAAATC 57.669 33.333 0.00 0.00 33.19 2.17
2725 6275 8.512138 TCTTTGCTGCTAGTTAAAGTAAAATCC 58.488 33.333 0.00 0.00 33.19 3.01
2728 6278 6.128391 TGCTGCTAGTTAAAGTAAAATCCGTG 60.128 38.462 0.00 0.00 0.00 4.94
2729 6279 6.128363 GCTGCTAGTTAAAGTAAAATCCGTGT 60.128 38.462 0.00 0.00 0.00 4.49
2730 6280 7.355332 TGCTAGTTAAAGTAAAATCCGTGTC 57.645 36.000 0.00 0.00 0.00 3.67
2731 6281 6.089820 TGCTAGTTAAAGTAAAATCCGTGTCG 59.910 38.462 0.00 0.00 0.00 4.35
2732 6282 6.089954 GCTAGTTAAAGTAAAATCCGTGTCGT 59.910 38.462 0.00 0.00 0.00 4.34
2733 6283 6.219302 AGTTAAAGTAAAATCCGTGTCGTG 57.781 37.500 0.00 0.00 0.00 4.35
2734 6284 3.531262 AAAGTAAAATCCGTGTCGTGC 57.469 42.857 0.00 0.00 0.00 5.34
2735 6285 2.450609 AGTAAAATCCGTGTCGTGCT 57.549 45.000 0.00 0.00 0.00 4.40
2736 6286 3.581024 AGTAAAATCCGTGTCGTGCTA 57.419 42.857 0.00 0.00 0.00 3.49
2737 6287 3.508762 AGTAAAATCCGTGTCGTGCTAG 58.491 45.455 0.00 0.00 0.00 3.42
2764 6314 1.328680 CAGCATTGCTAACTAGTGCCG 59.671 52.381 11.55 0.00 36.40 5.69
2766 6316 1.737793 GCATTGCTAACTAGTGCCGTT 59.262 47.619 0.16 0.00 0.00 4.44
2773 6323 4.096682 TGCTAACTAGTGCCGTTTTGTTTT 59.903 37.500 0.00 0.00 0.00 2.43
2774 6324 5.038683 GCTAACTAGTGCCGTTTTGTTTTT 58.961 37.500 0.00 0.00 0.00 1.94
2775 6325 5.051973 GCTAACTAGTGCCGTTTTGTTTTTG 60.052 40.000 0.00 0.00 0.00 2.44
2776 6326 4.443913 ACTAGTGCCGTTTTGTTTTTGT 57.556 36.364 0.00 0.00 0.00 2.83
2777 6327 4.811908 ACTAGTGCCGTTTTGTTTTTGTT 58.188 34.783 0.00 0.00 0.00 2.83
2778 6328 4.623595 ACTAGTGCCGTTTTGTTTTTGTTG 59.376 37.500 0.00 0.00 0.00 3.33
2779 6329 3.394719 AGTGCCGTTTTGTTTTTGTTGT 58.605 36.364 0.00 0.00 0.00 3.32
2831 6381 1.344763 GAGATCCCCATACTGGAACGG 59.655 57.143 0.00 0.00 40.96 4.44
2954 6504 2.460330 CACTGACCGTGCCAATCTC 58.540 57.895 0.00 0.00 36.72 2.75
2966 6516 1.865970 GCCAATCTCATCTCTTCTGCG 59.134 52.381 0.00 0.00 0.00 5.18
3063 6613 3.007831 TGGTTCATCTGTACTGTGCATCA 59.992 43.478 0.00 0.00 0.00 3.07
3107 6658 6.613153 ACTAACTCTCAAATTAGCTCCAGT 57.387 37.500 0.00 0.00 32.58 4.00
3108 6659 7.010339 ACTAACTCTCAAATTAGCTCCAGTT 57.990 36.000 0.00 0.00 32.58 3.16
3109 6660 6.876257 ACTAACTCTCAAATTAGCTCCAGTTG 59.124 38.462 0.00 0.00 32.58 3.16
3110 6661 4.583871 ACTCTCAAATTAGCTCCAGTTGG 58.416 43.478 0.00 0.00 0.00 3.77
3111 6662 4.287067 ACTCTCAAATTAGCTCCAGTTGGA 59.713 41.667 0.18 0.18 43.08 3.53
3246 6798 2.672996 CCAACCTTCAGTGCCGGG 60.673 66.667 2.18 0.00 0.00 5.73
3279 6831 1.358759 GGTGTCTGCGGTTTTGGTG 59.641 57.895 0.00 0.00 0.00 4.17
3296 6848 3.296854 TGGTGTCGCTAATAGAGGTGAT 58.703 45.455 0.00 0.00 0.00 3.06
3319 6871 2.009774 CCCTAATTGCTCGTTGACAGG 58.990 52.381 0.00 0.00 0.00 4.00
3321 6873 3.535561 CCTAATTGCTCGTTGACAGGAT 58.464 45.455 0.00 0.00 0.00 3.24
3489 7043 0.681733 TATCATCTTCGAGCCCTGGC 59.318 55.000 0.00 0.00 42.33 4.85
3587 7141 7.227156 AGTAATAATGCTCTATGAAACAGGGG 58.773 38.462 0.00 0.00 0.00 4.79
3655 7209 2.909244 CTGTCTCAGTGTAAGTTACGCG 59.091 50.000 18.38 3.53 43.64 6.01
3855 7415 6.107901 AGCTATCTGAACTGAACTGTCTTT 57.892 37.500 0.00 0.00 0.00 2.52
3856 7416 6.162777 AGCTATCTGAACTGAACTGTCTTTC 58.837 40.000 0.00 0.00 0.00 2.62
3857 7417 6.014669 AGCTATCTGAACTGAACTGTCTTTCT 60.015 38.462 0.00 0.00 0.00 2.52
3858 7418 6.648725 GCTATCTGAACTGAACTGTCTTTCTT 59.351 38.462 0.00 0.00 0.00 2.52
3859 7419 7.148656 GCTATCTGAACTGAACTGTCTTTCTTC 60.149 40.741 0.00 0.00 0.00 2.87
3860 7420 5.977635 TCTGAACTGAACTGTCTTTCTTCA 58.022 37.500 0.00 0.00 0.00 3.02
3864 7424 6.703607 TGAACTGAACTGTCTTTCTTCAGATC 59.296 38.462 12.41 10.55 42.36 2.75
3868 7428 7.387397 ACTGAACTGTCTTTCTTCAGATCATTC 59.613 37.037 12.41 0.00 42.36 2.67
3874 7434 8.728337 TGTCTTTCTTCAGATCATTCCTTATG 57.272 34.615 0.00 0.00 35.45 1.90
3885 7445 6.541641 AGATCATTCCTTATGCTGAGAAACAC 59.458 38.462 0.00 0.00 34.06 3.32
3887 7447 2.972625 TCCTTATGCTGAGAAACACCG 58.027 47.619 0.00 0.00 0.00 4.94
3888 7448 2.301870 TCCTTATGCTGAGAAACACCGT 59.698 45.455 0.00 0.00 0.00 4.83
3890 7450 4.161565 TCCTTATGCTGAGAAACACCGTAT 59.838 41.667 0.00 0.00 0.00 3.06
3892 7452 5.006746 CCTTATGCTGAGAAACACCGTATTC 59.993 44.000 0.00 0.00 0.00 1.75
3893 7453 2.695359 TGCTGAGAAACACCGTATTCC 58.305 47.619 0.00 0.00 0.00 3.01
3894 7454 2.301870 TGCTGAGAAACACCGTATTCCT 59.698 45.455 0.00 0.00 0.00 3.36
3895 7455 2.673368 GCTGAGAAACACCGTATTCCTG 59.327 50.000 0.00 0.00 0.00 3.86
3897 7457 4.566004 CTGAGAAACACCGTATTCCTGAA 58.434 43.478 0.00 0.00 0.00 3.02
3899 7459 4.202274 TGAGAAACACCGTATTCCTGAACA 60.202 41.667 0.00 0.00 0.00 3.18
3900 7460 4.710324 AGAAACACCGTATTCCTGAACAA 58.290 39.130 0.00 0.00 0.00 2.83
3901 7461 4.514066 AGAAACACCGTATTCCTGAACAAC 59.486 41.667 0.00 0.00 0.00 3.32
3902 7462 3.764237 ACACCGTATTCCTGAACAACT 57.236 42.857 0.00 0.00 0.00 3.16
3903 7463 3.660865 ACACCGTATTCCTGAACAACTC 58.339 45.455 0.00 0.00 0.00 3.01
3904 7464 3.000727 CACCGTATTCCTGAACAACTCC 58.999 50.000 0.00 0.00 0.00 3.85
3905 7465 2.635915 ACCGTATTCCTGAACAACTCCA 59.364 45.455 0.00 0.00 0.00 3.86
3906 7466 3.000727 CCGTATTCCTGAACAACTCCAC 58.999 50.000 0.00 0.00 0.00 4.02
3907 7467 3.306780 CCGTATTCCTGAACAACTCCACT 60.307 47.826 0.00 0.00 0.00 4.00
3913 7481 3.070159 TCCTGAACAACTCCACTCTCTTG 59.930 47.826 0.00 0.00 0.00 3.02
3975 7550 1.212751 GTTCACCATCTTTGCCGCC 59.787 57.895 0.00 0.00 0.00 6.13
4035 7610 1.068753 CCCCATCTGCTGCTACGAG 59.931 63.158 0.00 0.00 0.00 4.18
4054 7629 6.985188 ACGAGTACTATGTGCATTTGATTT 57.015 33.333 0.00 0.00 0.00 2.17
4291 8195 1.067060 TCTCTCTCTCTCTCTCGCTCG 59.933 57.143 0.00 0.00 0.00 5.03
4346 8250 4.072131 TGCCTGAACTCCACTTTAACATC 58.928 43.478 0.00 0.00 0.00 3.06
4483 8387 2.125912 CTGGAGGTGAAGGACGCG 60.126 66.667 3.53 3.53 0.00 6.01
4608 8512 1.505353 CTCCCTCGTAAACGCTCGT 59.495 57.895 0.00 0.00 39.60 4.18
4628 8543 3.694566 CGTGGGATAAAAGGAAGAAAGGG 59.305 47.826 0.00 0.00 0.00 3.95
4673 8588 4.799473 CATGTGCGCGGCTGTTCG 62.799 66.667 8.83 0.00 0.00 3.95
4737 8652 4.373156 ACCTCTAGCTGGTCATTGTTTT 57.627 40.909 0.00 0.00 31.03 2.43
4876 8811 3.069158 GCCTACCGTGGTGTGATATAGTT 59.931 47.826 0.72 0.00 0.00 2.24
5071 9009 4.359706 ACACAAAAACATTTCGAGGCTTC 58.640 39.130 0.00 0.00 0.00 3.86
5135 9083 6.417191 TTTCATAGTCCTGAAATTGTACGC 57.583 37.500 0.00 0.00 39.55 4.42
5136 9084 5.079689 TCATAGTCCTGAAATTGTACGCA 57.920 39.130 0.00 0.00 0.00 5.24
5137 9085 5.670485 TCATAGTCCTGAAATTGTACGCAT 58.330 37.500 0.00 0.00 0.00 4.73
5141 9089 5.428253 AGTCCTGAAATTGTACGCATACAT 58.572 37.500 0.00 0.00 41.02 2.29
5159 9107 7.571244 CGCATACATATCACATCCTTGTTTACC 60.571 40.741 0.00 0.00 32.34 2.85
5161 9109 8.777413 CATACATATCACATCCTTGTTTACCTG 58.223 37.037 0.00 0.00 32.34 4.00
5162 9110 6.721318 ACATATCACATCCTTGTTTACCTGT 58.279 36.000 0.00 0.00 32.34 4.00
5163 9111 7.857456 ACATATCACATCCTTGTTTACCTGTA 58.143 34.615 0.00 0.00 32.34 2.74
5164 9112 7.769044 ACATATCACATCCTTGTTTACCTGTAC 59.231 37.037 0.00 0.00 32.34 2.90
5169 9117 8.325787 TCACATCCTTGTTTACCTGTACATATT 58.674 33.333 0.00 0.00 32.34 1.28
5170 9118 8.956426 CACATCCTTGTTTACCTGTACATATTT 58.044 33.333 0.00 0.00 32.34 1.40
5225 9173 7.227992 TGAATTTTTCAAAATTTTCGACGCT 57.772 28.000 10.79 0.00 45.70 5.07
5231 9179 5.382573 TCAAAATTTTCGACGCTTTTTGG 57.617 34.783 15.97 3.88 37.68 3.28
5289 9238 0.035739 TCCAAAACGCCCCACTCTAC 59.964 55.000 0.00 0.00 0.00 2.59
5491 9441 7.231722 GCCAATACGGATATGTAGATCTCCTAT 59.768 40.741 0.00 0.00 36.56 2.57
5526 9476 2.188817 CTGTGTAACCCTAGCCCTCTT 58.811 52.381 0.00 0.00 34.36 2.85
5543 9493 5.010820 GCCCTCTTCGGTGTCTATATAAACT 59.989 44.000 0.00 0.00 0.00 2.66
5559 9509 3.520691 AAACTGGAGGGTTTTAGTCCC 57.479 47.619 0.00 0.00 44.90 4.46
5690 9640 3.175594 ACGTAGGGTTTTACCTCCATCA 58.824 45.455 0.00 0.00 42.09 3.07
5882 9833 1.006571 ATCAACAACGACGCGGTCT 60.007 52.632 12.47 0.00 0.00 3.85
5973 9924 2.910199 CCATCTGGAGCAGATCGAAAA 58.090 47.619 0.00 0.00 46.83 2.29
6053 10005 2.478200 GGAGACTTGATCTTCGACGGAC 60.478 54.545 0.00 0.00 38.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
465 472 1.792301 GTCTAAAAACGCCGCCTCC 59.208 57.895 0.00 0.00 0.00 4.30
466 473 1.418755 CGTCTAAAAACGCCGCCTC 59.581 57.895 0.00 0.00 35.64 4.70
572 588 4.649705 TCCCGGCCAAGGTCCAGA 62.650 66.667 2.24 0.00 0.00 3.86
583 599 2.722201 ATTGACGACTCCTCCCGGC 61.722 63.158 0.00 0.00 0.00 6.13
661 738 0.248866 GAACGCAAAAGGTGGTGGTG 60.249 55.000 0.00 0.00 0.00 4.17
662 739 1.388837 GGAACGCAAAAGGTGGTGGT 61.389 55.000 0.00 0.00 0.00 4.16
663 740 1.362355 GGAACGCAAAAGGTGGTGG 59.638 57.895 0.00 0.00 0.00 4.61
731 808 4.145876 TGTCGTGTCTTTCATCATTTGC 57.854 40.909 0.00 0.00 0.00 3.68
732 809 5.090757 CCATGTCGTGTCTTTCATCATTTG 58.909 41.667 0.00 0.00 0.00 2.32
836 922 3.993614 TACCGGCCGCTCCTACGAA 62.994 63.158 22.85 0.00 34.06 3.85
857 943 2.318578 CGTCGCACTGCATTTCATTTT 58.681 42.857 1.11 0.00 0.00 1.82
929 1020 1.058428 CCCTCCTCCATGCATCCTCA 61.058 60.000 0.00 0.00 0.00 3.86
961 1066 2.362397 GTCTGTGGAGTGAGACAGTGAA 59.638 50.000 0.00 0.00 40.48 3.18
962 1067 1.957177 GTCTGTGGAGTGAGACAGTGA 59.043 52.381 0.00 0.00 40.48 3.41
966 1071 1.179174 CCGGTCTGTGGAGTGAGACA 61.179 60.000 0.00 0.00 40.43 3.41
1042 1152 0.401738 TGGTGCCTCTCCTTTCCTTG 59.598 55.000 0.00 0.00 0.00 3.61
1092 1222 2.205022 AGCGTACCACTACACCACTA 57.795 50.000 0.00 0.00 0.00 2.74
1136 1270 0.663269 CAATCCGCGCTGCTACGATA 60.663 55.000 5.56 2.39 34.06 2.92
1178 1312 2.743928 GGTGGTGAGCAAGCGAGG 60.744 66.667 0.00 0.00 0.00 4.63
1189 1323 1.875009 CGAGGATGATGATGGTGGTG 58.125 55.000 0.00 0.00 0.00 4.17
1206 1340 1.152652 TTGGGGAAAAAGGCTGCGA 60.153 52.632 0.00 0.00 0.00 5.10
1315 1450 3.003173 CCCTTGTCCTCTGGCGGA 61.003 66.667 0.00 0.00 0.00 5.54
1332 1467 1.745489 GTGATCCCTTGTGACCGCC 60.745 63.158 0.00 0.00 0.00 6.13
1406 1541 1.080025 GTACCGCACTCCACAGGAC 60.080 63.158 0.00 0.00 0.00 3.85
1537 1687 1.448013 GCAGTACTCGAACCCCTGC 60.448 63.158 9.38 9.38 41.37 4.85
1585 1735 1.201429 AAGCATCCCCTTGTCGGAGT 61.201 55.000 0.00 0.00 31.41 3.85
1587 1737 1.299648 CAAGCATCCCCTTGTCGGA 59.700 57.895 0.00 0.00 37.89 4.55
1588 1738 3.909662 CAAGCATCCCCTTGTCGG 58.090 61.111 0.00 0.00 37.89 4.79
1592 1742 3.193479 GGTTAGAAACAAGCATCCCCTTG 59.807 47.826 0.72 0.72 45.90 3.61
1593 1743 3.431415 GGTTAGAAACAAGCATCCCCTT 58.569 45.455 0.00 0.00 0.00 3.95
1594 1744 2.291605 GGGTTAGAAACAAGCATCCCCT 60.292 50.000 0.00 0.00 0.00 4.79
1595 1745 2.100197 GGGTTAGAAACAAGCATCCCC 58.900 52.381 0.00 0.00 0.00 4.81
1597 1747 2.492088 GGTGGGTTAGAAACAAGCATCC 59.508 50.000 0.00 0.00 0.00 3.51
1598 1748 3.153919 TGGTGGGTTAGAAACAAGCATC 58.846 45.455 0.00 0.00 0.00 3.91
1599 1749 3.157087 CTGGTGGGTTAGAAACAAGCAT 58.843 45.455 0.00 0.00 0.00 3.79
1600 1750 2.582052 CTGGTGGGTTAGAAACAAGCA 58.418 47.619 0.00 0.00 0.00 3.91
1601 1751 1.269723 GCTGGTGGGTTAGAAACAAGC 59.730 52.381 0.00 0.00 0.00 4.01
1786 1949 4.702081 GAGGCGCACTCACGTCGT 62.702 66.667 10.83 0.00 45.85 4.34
1873 2041 0.108615 CCGAGGACACCATCAGACAC 60.109 60.000 0.00 0.00 0.00 3.67
1887 2055 2.587194 CGAGATGGCAAGCCGAGG 60.587 66.667 6.60 0.00 39.42 4.63
2063 2231 1.007848 CAGATATGGCTGCGAGCGAG 61.008 60.000 0.00 0.00 43.62 5.03
2072 2240 0.385751 CGTGGTCGTCAGATATGGCT 59.614 55.000 0.00 0.00 0.00 4.75
2079 2247 1.228033 TCACCTCGTGGTCGTCAGA 60.228 57.895 6.10 0.00 46.60 3.27
2122 2294 4.322080 TTCTGAATGTGCGGATACTAGG 57.678 45.455 0.00 0.00 0.00 3.02
2224 2396 3.119291 CTGAATGCTGGACGACACTATC 58.881 50.000 0.00 0.00 0.00 2.08
2233 2405 3.488778 AGGATGATCTGAATGCTGGAC 57.511 47.619 0.00 0.00 0.00 4.02
2301 2484 9.806203 ACGCAACATGTTAATACTACTAATACA 57.194 29.630 11.53 0.00 0.00 2.29
2305 2488 6.814644 AGCACGCAACATGTTAATACTACTAA 59.185 34.615 11.53 0.00 0.00 2.24
2308 5857 5.255596 CAGCACGCAACATGTTAATACTAC 58.744 41.667 11.53 0.00 0.00 2.73
2314 5863 3.470520 GCAGCACGCAACATGTTAA 57.529 47.368 11.53 0.00 41.79 2.01
2493 6043 6.038050 GCCAAATTGAGAAACACCAAATGAAA 59.962 34.615 0.00 0.00 0.00 2.69
2550 6100 1.001633 GACGTGCCACCTTTCTAGGAA 59.998 52.381 0.00 0.00 45.05 3.36
2691 6241 0.038166 TAGCAGCAAAGACTTGGGGG 59.962 55.000 0.00 0.00 32.76 5.40
2694 6244 5.239525 ACTTTAACTAGCAGCAAAGACTTGG 59.760 40.000 8.71 0.00 33.29 3.61
2695 6245 6.305693 ACTTTAACTAGCAGCAAAGACTTG 57.694 37.500 8.71 0.00 33.29 3.16
2696 6246 8.446599 TTTACTTTAACTAGCAGCAAAGACTT 57.553 30.769 8.71 0.00 33.29 3.01
2697 6247 8.446599 TTTTACTTTAACTAGCAGCAAAGACT 57.553 30.769 8.71 0.00 33.29 3.24
2698 6248 9.331106 GATTTTACTTTAACTAGCAGCAAAGAC 57.669 33.333 8.71 0.00 33.29 3.01
2700 6250 7.481798 CGGATTTTACTTTAACTAGCAGCAAAG 59.518 37.037 0.00 0.00 34.80 2.77
2701 6251 7.040961 ACGGATTTTACTTTAACTAGCAGCAAA 60.041 33.333 0.00 0.00 0.00 3.68
2702 6252 6.428771 ACGGATTTTACTTTAACTAGCAGCAA 59.571 34.615 0.00 0.00 0.00 3.91
2703 6253 5.935789 ACGGATTTTACTTTAACTAGCAGCA 59.064 36.000 0.00 0.00 0.00 4.41
2704 6254 6.128363 ACACGGATTTTACTTTAACTAGCAGC 60.128 38.462 0.00 0.00 0.00 5.25
2705 6255 7.360575 ACACGGATTTTACTTTAACTAGCAG 57.639 36.000 0.00 0.00 0.00 4.24
2709 6259 6.128849 GCACGACACGGATTTTACTTTAACTA 60.129 38.462 0.00 0.00 0.00 2.24
2717 6267 2.601763 CCTAGCACGACACGGATTTTAC 59.398 50.000 0.00 0.00 0.00 2.01
2724 6274 0.038526 AACTTCCTAGCACGACACGG 60.039 55.000 0.00 0.00 0.00 4.94
2725 6275 1.335597 TGAACTTCCTAGCACGACACG 60.336 52.381 0.00 0.00 0.00 4.49
2728 6278 1.336887 TGCTGAACTTCCTAGCACGAC 60.337 52.381 0.00 0.00 42.05 4.34
2729 6279 0.966179 TGCTGAACTTCCTAGCACGA 59.034 50.000 0.00 0.00 42.05 4.35
2730 6280 3.514777 TGCTGAACTTCCTAGCACG 57.485 52.632 0.00 0.00 42.05 5.34
2733 6283 2.363683 AGCAATGCTGAACTTCCTAGC 58.636 47.619 7.07 0.00 37.57 3.42
2734 6284 5.181748 AGTTAGCAATGCTGAACTTCCTAG 58.818 41.667 19.25 0.00 40.10 3.02
2735 6285 5.165961 AGTTAGCAATGCTGAACTTCCTA 57.834 39.130 19.25 0.00 40.10 2.94
2736 6286 4.026356 AGTTAGCAATGCTGAACTTCCT 57.974 40.909 19.25 0.00 40.10 3.36
2737 6287 4.938226 ACTAGTTAGCAATGCTGAACTTCC 59.062 41.667 24.06 6.09 40.10 3.46
2774 6324 9.725019 ACATTCTTCAGATACTGATAAACAACA 57.275 29.630 2.30 0.00 40.39 3.33
2831 6381 4.363999 CGATACAGATGAACAGGGAGAAC 58.636 47.826 0.00 0.00 0.00 3.01
2954 6504 0.463295 ACCATGGCGCAGAAGAGATG 60.463 55.000 13.04 0.00 0.00 2.90
2966 6516 1.960040 GCAAAGGGGCTAACCATGGC 61.960 60.000 13.04 0.00 42.91 4.40
3081 6631 8.763601 ACTGGAGCTAATTTGAGAGTTAGTATT 58.236 33.333 0.00 0.00 31.98 1.89
3082 6632 8.312669 ACTGGAGCTAATTTGAGAGTTAGTAT 57.687 34.615 0.00 0.00 31.98 2.12
3085 6635 6.314896 CCAACTGGAGCTAATTTGAGAGTTAG 59.685 42.308 0.00 0.00 37.39 2.34
3137 6689 9.632969 CGAAACTCAACCGAATAATAAGTAATG 57.367 33.333 0.00 0.00 0.00 1.90
3246 6798 1.326548 GACACCATACCGAACGATTGC 59.673 52.381 0.00 0.00 0.00 3.56
3279 6831 3.193056 GGGGTATCACCTCTATTAGCGAC 59.807 52.174 0.00 0.00 35.29 5.19
3296 6848 2.568062 TGTCAACGAGCAATTAGGGGTA 59.432 45.455 0.00 0.00 0.00 3.69
3319 6871 9.890352 GACTAAATTGCATAGAAGAAATGGATC 57.110 33.333 0.00 0.00 0.00 3.36
3321 6873 7.552687 ACGACTAAATTGCATAGAAGAAATGGA 59.447 33.333 0.00 0.00 0.00 3.41
3489 7043 9.823098 CATTCAGAACAGAGAAGAATAAAACAG 57.177 33.333 0.00 0.00 0.00 3.16
3579 7133 3.305181 GGATGCCAATCCCCTGTTT 57.695 52.632 0.00 0.00 46.03 2.83
3587 7141 1.753073 CCACAAAGGAGGATGCCAATC 59.247 52.381 0.00 0.00 41.22 2.67
3855 7415 6.325804 TCTCAGCATAAGGAATGATCTGAAGA 59.674 38.462 0.00 0.00 35.54 2.87
3856 7416 6.522946 TCTCAGCATAAGGAATGATCTGAAG 58.477 40.000 0.00 0.00 35.54 3.02
3857 7417 6.490241 TCTCAGCATAAGGAATGATCTGAA 57.510 37.500 0.00 0.00 35.54 3.02
3858 7418 6.490241 TTCTCAGCATAAGGAATGATCTGA 57.510 37.500 0.00 0.00 37.86 3.27
3859 7419 6.541278 TGTTTCTCAGCATAAGGAATGATCTG 59.459 38.462 0.00 0.00 37.86 2.90
3860 7420 6.541641 GTGTTTCTCAGCATAAGGAATGATCT 59.458 38.462 0.00 0.00 37.86 2.75
3864 7424 4.201851 CGGTGTTTCTCAGCATAAGGAATG 60.202 45.833 0.00 0.00 43.83 2.67
3868 7428 2.699954 ACGGTGTTTCTCAGCATAAGG 58.300 47.619 0.00 0.00 43.83 2.69
3874 7434 2.673368 CAGGAATACGGTGTTTCTCAGC 59.327 50.000 0.00 0.00 40.68 4.26
3885 7445 3.000727 GTGGAGTTGTTCAGGAATACGG 58.999 50.000 0.00 0.00 0.00 4.02
3887 7447 5.046950 AGAGAGTGGAGTTGTTCAGGAATAC 60.047 44.000 0.00 0.00 0.00 1.89
3888 7448 5.087323 AGAGAGTGGAGTTGTTCAGGAATA 58.913 41.667 0.00 0.00 0.00 1.75
3890 7450 3.309296 AGAGAGTGGAGTTGTTCAGGAA 58.691 45.455 0.00 0.00 0.00 3.36
3892 7452 3.181461 ACAAGAGAGTGGAGTTGTTCAGG 60.181 47.826 0.00 0.00 28.62 3.86
3893 7453 4.065321 ACAAGAGAGTGGAGTTGTTCAG 57.935 45.455 0.00 0.00 28.62 3.02
3894 7454 5.304357 TGATACAAGAGAGTGGAGTTGTTCA 59.696 40.000 0.00 0.00 34.92 3.18
3895 7455 5.784177 TGATACAAGAGAGTGGAGTTGTTC 58.216 41.667 0.00 0.00 34.92 3.18
3897 7457 5.247110 ACATGATACAAGAGAGTGGAGTTGT 59.753 40.000 0.00 0.00 37.00 3.32
3899 7459 5.728471 CACATGATACAAGAGAGTGGAGTT 58.272 41.667 0.00 0.00 0.00 3.01
3900 7460 4.382470 GCACATGATACAAGAGAGTGGAGT 60.382 45.833 0.00 0.00 0.00 3.85
3901 7461 4.118410 GCACATGATACAAGAGAGTGGAG 58.882 47.826 0.00 0.00 0.00 3.86
3902 7462 3.515104 TGCACATGATACAAGAGAGTGGA 59.485 43.478 0.00 0.00 0.00 4.02
3903 7463 3.865446 TGCACATGATACAAGAGAGTGG 58.135 45.455 0.00 0.00 0.00 4.00
3904 7464 3.869832 CCTGCACATGATACAAGAGAGTG 59.130 47.826 0.00 0.00 0.00 3.51
3905 7465 3.118482 CCCTGCACATGATACAAGAGAGT 60.118 47.826 0.00 0.00 0.00 3.24
3906 7466 3.133542 TCCCTGCACATGATACAAGAGAG 59.866 47.826 0.00 0.00 0.00 3.20
3907 7467 3.106827 TCCCTGCACATGATACAAGAGA 58.893 45.455 0.00 0.00 0.00 3.10
3913 7481 4.402155 TCCAAATTTCCCTGCACATGATAC 59.598 41.667 0.00 0.00 0.00 2.24
4035 7610 5.965334 CCGTCAAATCAAATGCACATAGTAC 59.035 40.000 0.00 0.00 0.00 2.73
4054 7629 0.892755 AGCGATTAACCAGACCGTCA 59.107 50.000 0.40 0.00 0.00 4.35
4267 7844 2.546795 GCGAGAGAGAGAGAGAGAGAGG 60.547 59.091 0.00 0.00 0.00 3.69
4291 8195 1.529865 GTTTTGACCACTACGAGCCAC 59.470 52.381 0.00 0.00 0.00 5.01
4369 8273 0.664761 ACTGCAAGCACACATGTCAC 59.335 50.000 0.00 0.00 37.60 3.67
4378 8282 0.657840 AGTCGTTGAACTGCAAGCAC 59.342 50.000 0.00 0.00 37.60 4.40
4382 8286 3.723260 TGATGTAGTCGTTGAACTGCAA 58.277 40.909 0.00 0.00 43.60 4.08
4608 8512 3.076785 TGCCCTTTCTTCCTTTTATCCCA 59.923 43.478 0.00 0.00 0.00 4.37
4628 8543 2.297033 TCAGCCAAGAAAGAAACCATGC 59.703 45.455 0.00 0.00 0.00 4.06
4673 8588 1.079503 GCTCAACAACACTCGGATCC 58.920 55.000 0.00 0.00 0.00 3.36
4678 8593 0.583438 CCACTGCTCAACAACACTCG 59.417 55.000 0.00 0.00 0.00 4.18
4757 8672 7.565398 ACCCCGATCTACAAGCATATAGATAAT 59.435 37.037 0.00 0.00 38.09 1.28
4876 8811 0.539986 GCATTTCGGGAGGGAGTACA 59.460 55.000 0.00 0.00 0.00 2.90
4917 8853 4.270245 TCATTTCAAATTTGGCCTCCAC 57.730 40.909 17.90 0.00 30.78 4.02
4980 8917 6.003326 TGCATGTCTTTATGTATATGTGGGG 58.997 40.000 0.00 0.00 0.00 4.96
4981 8918 6.486320 TGTGCATGTCTTTATGTATATGTGGG 59.514 38.462 0.00 0.00 0.00 4.61
4982 8919 7.495135 TGTGCATGTCTTTATGTATATGTGG 57.505 36.000 0.00 0.00 0.00 4.17
4991 8928 8.572828 TTTACAAACTTGTGCATGTCTTTATG 57.427 30.769 5.34 0.00 42.31 1.90
4992 8929 9.762933 AATTTACAAACTTGTGCATGTCTTTAT 57.237 25.926 5.34 0.00 42.31 1.40
5034 8972 9.762933 ATGTTTTTGTGTAGCACTCATTTTAAT 57.237 25.926 0.90 0.00 35.11 1.40
5071 9009 8.417106 TCAGGAAGAATAGTGCATCTACTTAAG 58.583 37.037 0.00 0.00 32.19 1.85
5130 9078 5.926542 ACAAGGATGTGATATGTATGCGTAC 59.073 40.000 9.25 9.25 38.69 3.67
5134 9082 7.445402 AGGTAAACAAGGATGTGATATGTATGC 59.555 37.037 0.00 0.00 40.46 3.14
5135 9083 8.777413 CAGGTAAACAAGGATGTGATATGTATG 58.223 37.037 0.00 0.00 40.46 2.39
5136 9084 8.494433 ACAGGTAAACAAGGATGTGATATGTAT 58.506 33.333 0.00 0.00 40.46 2.29
5137 9085 7.857456 ACAGGTAAACAAGGATGTGATATGTA 58.143 34.615 0.00 0.00 40.46 2.29
5141 9089 7.247456 TGTACAGGTAAACAAGGATGTGATA 57.753 36.000 0.00 0.00 40.46 2.15
5202 9150 8.528432 AAAGCGTCGAAAATTTTGAAAAATTC 57.472 26.923 8.47 8.56 45.16 2.17
5205 9153 7.269297 CCAAAAAGCGTCGAAAATTTTGAAAAA 59.731 29.630 19.89 0.00 41.26 1.94
5231 9179 6.745907 GGAGGCCGATTTATTTATTTTATCGC 59.254 38.462 0.00 0.00 37.39 4.58
5234 9182 9.927668 CAATGGAGGCCGATTTATTTATTTTAT 57.072 29.630 0.00 0.00 0.00 1.40
5235 9183 9.137459 TCAATGGAGGCCGATTTATTTATTTTA 57.863 29.630 0.00 0.00 0.00 1.52
5265 9214 2.282180 GGGGCGTTTTGGAGCTCA 60.282 61.111 17.19 0.00 35.08 4.26
5289 9238 2.290323 CGCCTTAGATAATGGAAGGGGG 60.290 54.545 8.63 0.00 45.09 5.40
5436 9386 0.472471 TTCCACGCCAAGGAAAGTCT 59.528 50.000 0.00 0.00 41.94 3.24
5466 9416 8.698973 ATAGGAGATCTACATATCCGTATTGG 57.301 38.462 7.93 0.00 44.22 3.16
5491 9441 5.224888 GTTACACAGAGTCGGTTACAATGA 58.775 41.667 0.00 0.00 0.00 2.57
5526 9476 4.831155 CCCTCCAGTTTATATAGACACCGA 59.169 45.833 6.22 0.00 0.00 4.69
5559 9509 5.902681 TGGTATGATTGTTCTTCGTCCTAG 58.097 41.667 0.00 0.00 0.00 3.02
5569 9519 5.799213 AGCTAGCCTATGGTATGATTGTTC 58.201 41.667 12.13 0.00 0.00 3.18
5690 9640 3.330720 CCAGGTTCGGGCCCTCTT 61.331 66.667 22.43 3.59 0.00 2.85
5882 9833 2.547218 CGGAGAGAAAAGTTTCGTCCCA 60.547 50.000 16.45 0.00 39.80 4.37


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

AutoCloner maintained by Alex Coulton.