Multiple sequence alignment - TraesCS7D01G405300

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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 TraesCS7D01G405300 chr7D 100.000 4272 0 0 1 4272 522870987 522875258 0.000000e+00 7890.0
1 TraesCS7D01G405300 chr7D 86.340 1508 183 6 1747 3241 523437321 523438818 0.000000e+00 1622.0
2 TraesCS7D01G405300 chr7D 84.164 1484 168 27 1799 3270 523277258 523275830 0.000000e+00 1376.0
3 TraesCS7D01G405300 chr7D 85.837 812 113 2 2447 3257 523269155 523268345 0.000000e+00 861.0
4 TraesCS7D01G405300 chr7D 85.902 610 65 5 2661 3270 523486879 523487467 7.800000e-177 630.0
5 TraesCS7D01G405300 chr7D 83.832 334 41 6 1331 1652 523436924 523437256 5.370000e-79 305.0
6 TraesCS7D01G405300 chr7D 87.879 231 28 0 1332 1562 523277549 523277319 5.440000e-69 272.0
7 TraesCS7D01G405300 chr7D 87.556 225 28 0 1332 1556 523486216 523486440 1.180000e-65 261.0
8 TraesCS7D01G405300 chr7D 87.898 157 16 3 660 815 633367065 633366911 9.440000e-42 182.0
9 TraesCS7D01G405300 chr7D 81.707 164 28 2 1379 1541 523270641 523270479 7.450000e-28 135.0
10 TraesCS7D01G405300 chr7B 94.914 1927 81 4 1325 3251 556687135 556689044 0.000000e+00 3000.0
11 TraesCS7D01G405300 chr7B 85.847 1512 200 5 1769 3270 558642073 558640566 0.000000e+00 1594.0
12 TraesCS7D01G405300 chr7B 84.028 1584 189 22 1695 3270 558365229 558363702 0.000000e+00 1465.0
13 TraesCS7D01G405300 chr7B 94.551 679 22 11 1 666 556684968 556685644 0.000000e+00 1035.0
14 TraesCS7D01G405300 chr7B 94.266 436 17 2 874 1301 556686602 556687037 0.000000e+00 660.0
15 TraesCS7D01G405300 chr7B 79.504 605 78 24 998 1560 558642795 558642195 5.180000e-104 388.0
16 TraesCS7D01G405300 chr7A 84.601 1578 202 25 1700 3247 603960432 603958866 0.000000e+00 1530.0
17 TraesCS7D01G405300 chr7A 83.612 1495 182 28 1766 3247 603945307 603943863 0.000000e+00 1345.0
18 TraesCS7D01G405300 chr7A 93.452 840 52 3 2414 3251 603025342 603026180 0.000000e+00 1243.0
19 TraesCS7D01G405300 chr7A 94.811 636 33 0 1750 2385 603024569 603025204 0.000000e+00 992.0
20 TraesCS7D01G405300 chr7A 90.678 472 38 4 9 477 603023079 603023547 1.300000e-174 623.0
21 TraesCS7D01G405300 chr7A 95.238 378 18 0 925 1302 603023774 603024151 2.200000e-167 599.0
22 TraesCS7D01G405300 chr7A 92.284 324 22 1 1325 1648 603024248 603024568 1.400000e-124 457.0
23 TraesCS7D01G405300 chr7A 89.316 234 25 0 1331 1564 603960748 603960515 1.160000e-75 294.0
24 TraesCS7D01G405300 chr7A 88.646 229 26 0 1332 1560 603945557 603945329 3.250000e-71 279.0
25 TraesCS7D01G405300 chr7A 81.667 120 18 1 998 1113 603961153 603961034 3.520000e-16 97.1
26 TraesCS7D01G405300 chr3A 92.823 1031 60 8 3253 4272 279426523 279427550 0.000000e+00 1482.0
27 TraesCS7D01G405300 chr5A 92.449 1033 62 8 3253 4272 32722465 32721436 0.000000e+00 1461.0
28 TraesCS7D01G405300 chr5A 91.957 1032 68 7 3253 4272 457527418 457528446 0.000000e+00 1432.0
29 TraesCS7D01G405300 chr5A 91.553 1030 70 10 3256 4272 689173200 689172175 0.000000e+00 1404.0
30 TraesCS7D01G405300 chr5A 85.963 1033 120 16 3257 4272 402032602 402033626 0.000000e+00 1081.0
31 TraesCS7D01G405300 chr5A 89.583 48 3 2 423 469 631716760 631716806 4.610000e-05 60.2
32 TraesCS7D01G405300 chr6A 92.144 1031 64 10 3255 4272 61874326 61873300 0.000000e+00 1439.0
33 TraesCS7D01G405300 chr2B 91.094 1033 77 8 3253 4272 63217262 63216232 0.000000e+00 1384.0
34 TraesCS7D01G405300 chr2B 87.331 1034 103 20 3253 4272 256967338 256968357 0.000000e+00 1158.0
35 TraesCS7D01G405300 chr2B 82.037 1041 129 26 3255 4272 103432589 103431584 0.000000e+00 833.0
36 TraesCS7D01G405300 chr2B 88.364 275 17 8 3253 3514 63187627 63187355 2.480000e-82 316.0
37 TraesCS7D01G405300 chr2B 91.837 147 11 1 660 805 306906285 306906431 2.010000e-48 204.0
38 TraesCS7D01G405300 chr2B 86.408 103 14 0 4170 4272 187499483 187499381 3.490000e-21 113.0
39 TraesCS7D01G405300 chr5D 85.700 1035 118 20 3253 4266 45119389 45120414 0.000000e+00 1064.0
40 TraesCS7D01G405300 chr5D 85.246 1037 121 22 3253 4266 292136538 292137565 0.000000e+00 1038.0
41 TraesCS7D01G405300 chr5D 79.558 181 18 11 423 594 503960965 503961135 1.260000e-20 111.0
42 TraesCS7D01G405300 chr5D 77.301 163 25 9 426 582 371473390 371473546 7.610000e-13 86.1
43 TraesCS7D01G405300 chr3B 85.300 1034 124 17 3253 4266 754567295 754568320 0.000000e+00 1042.0
44 TraesCS7D01G405300 chr3B 83.173 1040 141 24 3253 4269 642196202 642197230 0.000000e+00 920.0
45 TraesCS7D01G405300 chr3B 85.036 274 27 7 3253 3513 754616486 754616758 2.530000e-67 267.0
46 TraesCS7D01G405300 chr3B 84.513 226 20 8 3253 3466 754507755 754507977 4.330000e-50 209.0
47 TraesCS7D01G405300 chr3B 86.145 166 19 3 667 829 637530587 637530751 4.390000e-40 176.0
48 TraesCS7D01G405300 chr2D 88.199 161 16 3 660 817 20424699 20424539 5.640000e-44 189.0
49 TraesCS7D01G405300 chr2D 89.552 67 7 0 6 72 648383945 648384011 7.610000e-13 86.1
50 TraesCS7D01G405300 chr4D 87.821 156 16 2 660 814 215464631 215464478 3.390000e-41 180.0
51 TraesCS7D01G405300 chr4B 89.437 142 15 0 667 808 57172182 57172323 3.390000e-41 180.0
52 TraesCS7D01G405300 chr4B 89.706 136 13 1 679 814 68406918 68406784 5.680000e-39 172.0
53 TraesCS7D01G405300 chr2A 88.000 150 15 2 660 808 236829302 236829155 1.580000e-39 174.0
54 TraesCS7D01G405300 chr4A 88.276 145 14 3 666 808 552076896 552077039 2.040000e-38 171.0


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 TraesCS7D01G405300 chr7D 522870987 522875258 4271 False 7890.000000 7890 100.000000 1 4272 1 chr7D.!!$F1 4271
1 TraesCS7D01G405300 chr7D 523436924 523438818 1894 False 963.500000 1622 85.086000 1331 3241 2 chr7D.!!$F2 1910
2 TraesCS7D01G405300 chr7D 523275830 523277549 1719 True 824.000000 1376 86.021500 1332 3270 2 chr7D.!!$R3 1938
3 TraesCS7D01G405300 chr7D 523268345 523270641 2296 True 498.000000 861 83.772000 1379 3257 2 chr7D.!!$R2 1878
4 TraesCS7D01G405300 chr7D 523486216 523487467 1251 False 445.500000 630 86.729000 1332 3270 2 chr7D.!!$F3 1938
5 TraesCS7D01G405300 chr7B 556684968 556689044 4076 False 1565.000000 3000 94.577000 1 3251 3 chr7B.!!$F1 3250
6 TraesCS7D01G405300 chr7B 558363702 558365229 1527 True 1465.000000 1465 84.028000 1695 3270 1 chr7B.!!$R1 1575
7 TraesCS7D01G405300 chr7B 558640566 558642795 2229 True 991.000000 1594 82.675500 998 3270 2 chr7B.!!$R2 2272
8 TraesCS7D01G405300 chr7A 603943863 603945557 1694 True 812.000000 1345 86.129000 1332 3247 2 chr7A.!!$R1 1915
9 TraesCS7D01G405300 chr7A 603023079 603026180 3101 False 782.800000 1243 93.292600 9 3251 5 chr7A.!!$F1 3242
10 TraesCS7D01G405300 chr7A 603958866 603961153 2287 True 640.366667 1530 85.194667 998 3247 3 chr7A.!!$R2 2249
11 TraesCS7D01G405300 chr3A 279426523 279427550 1027 False 1482.000000 1482 92.823000 3253 4272 1 chr3A.!!$F1 1019
12 TraesCS7D01G405300 chr5A 32721436 32722465 1029 True 1461.000000 1461 92.449000 3253 4272 1 chr5A.!!$R1 1019
13 TraesCS7D01G405300 chr5A 457527418 457528446 1028 False 1432.000000 1432 91.957000 3253 4272 1 chr5A.!!$F2 1019
14 TraesCS7D01G405300 chr5A 689172175 689173200 1025 True 1404.000000 1404 91.553000 3256 4272 1 chr5A.!!$R2 1016
15 TraesCS7D01G405300 chr5A 402032602 402033626 1024 False 1081.000000 1081 85.963000 3257 4272 1 chr5A.!!$F1 1015
16 TraesCS7D01G405300 chr6A 61873300 61874326 1026 True 1439.000000 1439 92.144000 3255 4272 1 chr6A.!!$R1 1017
17 TraesCS7D01G405300 chr2B 63216232 63217262 1030 True 1384.000000 1384 91.094000 3253 4272 1 chr2B.!!$R2 1019
18 TraesCS7D01G405300 chr2B 256967338 256968357 1019 False 1158.000000 1158 87.331000 3253 4272 1 chr2B.!!$F1 1019
19 TraesCS7D01G405300 chr2B 103431584 103432589 1005 True 833.000000 833 82.037000 3255 4272 1 chr2B.!!$R3 1017
20 TraesCS7D01G405300 chr5D 45119389 45120414 1025 False 1064.000000 1064 85.700000 3253 4266 1 chr5D.!!$F1 1013
21 TraesCS7D01G405300 chr5D 292136538 292137565 1027 False 1038.000000 1038 85.246000 3253 4266 1 chr5D.!!$F2 1013
22 TraesCS7D01G405300 chr3B 754567295 754568320 1025 False 1042.000000 1042 85.300000 3253 4266 1 chr3B.!!$F4 1013
23 TraesCS7D01G405300 chr3B 642196202 642197230 1028 False 920.000000 920 83.173000 3253 4269 1 chr3B.!!$F2 1016

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
817 898 0.034337 GGCCGGGGGTTTTTCTTTTC 59.966 55.000 2.18 0.00 0.00 2.29 F
917 1933 1.001158 CGCCTAGCTAGCTACAGTTCC 60.001 57.143 20.67 4.12 0.00 3.62 F
996 2020 1.153823 CGTACGGTCCCAAGCTCTG 60.154 63.158 7.57 0.00 0.00 3.35 F
2464 4257 0.170561 GTGCTGCTTGCTTGATCAGG 59.829 55.000 0.00 0.00 43.37 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 3740 0.324943 CGGAGATCAGGGGTGTGTTT 59.675 55.000 0.00 0.0 0.00 2.83 R
2464 4257 1.285950 GGCGGCCTTGTCAAAGAAC 59.714 57.895 12.87 0.0 35.19 3.01 R
2750 4543 1.742268 GTCGTAGAGCGGAACTAAGGT 59.258 52.381 0.00 0.0 41.72 3.50 R
3337 5132 0.180406 AAGCCGTGTTCCACTTGTCT 59.820 50.000 0.00 0.0 31.34 3.41 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
137 141 6.604171 ACTTAATGGTGAGGCATGATGATAA 58.396 36.000 0.00 0.00 0.00 1.75
146 150 6.712095 GTGAGGCATGATGATAAACCTATGAA 59.288 38.462 0.00 0.00 0.00 2.57
169 173 3.963129 TGACAAAGGAAACTCACAAGGT 58.037 40.909 0.00 0.00 42.68 3.50
281 288 6.392625 TTGTCTTGATAAGTATCCTCTCCG 57.607 41.667 0.00 0.00 31.71 4.63
301 308 4.101898 TCCGCCTGAACTATTTTAGCCATA 59.898 41.667 0.00 0.00 0.00 2.74
480 558 9.722056 CACAGTAAAATGACATTTATAGAAGCC 57.278 33.333 13.69 0.00 0.00 4.35
481 559 8.612619 ACAGTAAAATGACATTTATAGAAGCCG 58.387 33.333 13.69 0.16 0.00 5.52
482 560 8.612619 CAGTAAAATGACATTTATAGAAGCCGT 58.387 33.333 13.69 0.00 0.00 5.68
483 561 8.612619 AGTAAAATGACATTTATAGAAGCCGTG 58.387 33.333 13.69 0.00 0.00 4.94
484 562 7.624360 AAAATGACATTTATAGAAGCCGTGA 57.376 32.000 13.69 0.00 0.00 4.35
485 563 6.604735 AATGACATTTATAGAAGCCGTGAC 57.395 37.500 0.00 0.00 0.00 3.67
486 564 5.079689 TGACATTTATAGAAGCCGTGACA 57.920 39.130 0.00 0.00 0.00 3.58
487 565 5.483811 TGACATTTATAGAAGCCGTGACAA 58.516 37.500 0.00 0.00 0.00 3.18
488 566 5.935206 TGACATTTATAGAAGCCGTGACAAA 59.065 36.000 0.00 0.00 0.00 2.83
489 567 6.092122 TGACATTTATAGAAGCCGTGACAAAG 59.908 38.462 0.00 0.00 0.00 2.77
490 568 6.170506 ACATTTATAGAAGCCGTGACAAAGA 58.829 36.000 0.00 0.00 0.00 2.52
491 569 6.823689 ACATTTATAGAAGCCGTGACAAAGAT 59.176 34.615 0.00 0.00 0.00 2.40
492 570 7.985184 ACATTTATAGAAGCCGTGACAAAGATA 59.015 33.333 0.00 0.00 0.00 1.98
493 571 8.826710 CATTTATAGAAGCCGTGACAAAGATAA 58.173 33.333 0.00 0.00 0.00 1.75
494 572 8.780846 TTTATAGAAGCCGTGACAAAGATAAA 57.219 30.769 0.00 0.00 0.00 1.40
495 573 8.958119 TTATAGAAGCCGTGACAAAGATAAAT 57.042 30.769 0.00 0.00 0.00 1.40
497 575 8.958119 ATAGAAGCCGTGACAAAGATAAATAA 57.042 30.769 0.00 0.00 0.00 1.40
498 576 7.681939 AGAAGCCGTGACAAAGATAAATAAA 57.318 32.000 0.00 0.00 0.00 1.40
499 577 8.106247 AGAAGCCGTGACAAAGATAAATAAAA 57.894 30.769 0.00 0.00 0.00 1.52
500 578 8.573035 AGAAGCCGTGACAAAGATAAATAAAAA 58.427 29.630 0.00 0.00 0.00 1.94
501 579 9.353999 GAAGCCGTGACAAAGATAAATAAAAAT 57.646 29.630 0.00 0.00 0.00 1.82
502 580 8.911247 AGCCGTGACAAAGATAAATAAAAATC 57.089 30.769 0.00 0.00 0.00 2.17
503 581 8.519526 AGCCGTGACAAAGATAAATAAAAATCA 58.480 29.630 0.00 0.00 0.00 2.57
504 582 9.134734 GCCGTGACAAAGATAAATAAAAATCAA 57.865 29.630 0.00 0.00 0.00 2.57
542 620 8.899427 TTTTTAAATGCATTTTGGAGTGATGA 57.101 26.923 28.45 4.97 0.00 2.92
590 670 8.422973 TGCCATTTCATTATGAATTTACAAGC 57.577 30.769 8.56 6.18 36.11 4.01
673 754 8.604035 TGAAATTTACTGTTCATCTTAGATCGC 58.396 33.333 0.00 0.00 0.00 4.58
675 756 3.085443 ACTGTTCATCTTAGATCGCCG 57.915 47.619 0.00 0.00 0.00 6.46
676 757 2.223829 ACTGTTCATCTTAGATCGCCGG 60.224 50.000 0.00 0.00 0.00 6.13
677 758 1.068588 TGTTCATCTTAGATCGCCGGG 59.931 52.381 2.18 0.00 0.00 5.73
678 759 1.068741 GTTCATCTTAGATCGCCGGGT 59.931 52.381 2.18 0.00 0.00 5.28
679 760 0.673985 TCATCTTAGATCGCCGGGTG 59.326 55.000 2.18 0.00 0.00 4.61
680 761 0.389391 CATCTTAGATCGCCGGGTGT 59.611 55.000 2.18 0.00 0.00 4.16
681 762 0.389391 ATCTTAGATCGCCGGGTGTG 59.611 55.000 2.18 0.00 0.00 3.82
682 763 1.227263 CTTAGATCGCCGGGTGTGG 60.227 63.158 2.18 0.00 0.00 4.17
683 764 1.672854 CTTAGATCGCCGGGTGTGGA 61.673 60.000 2.18 0.00 0.00 4.02
684 765 1.672854 TTAGATCGCCGGGTGTGGAG 61.673 60.000 2.18 0.00 0.00 3.86
689 770 2.597510 GCCGGGTGTGGAGCTTTT 60.598 61.111 2.18 0.00 0.00 2.27
690 771 2.626780 GCCGGGTGTGGAGCTTTTC 61.627 63.158 2.18 0.00 0.00 2.29
691 772 1.228124 CCGGGTGTGGAGCTTTTCA 60.228 57.895 0.00 0.00 0.00 2.69
692 773 1.237285 CCGGGTGTGGAGCTTTTCAG 61.237 60.000 0.00 0.00 0.00 3.02
693 774 0.250295 CGGGTGTGGAGCTTTTCAGA 60.250 55.000 0.00 0.00 0.00 3.27
694 775 1.611673 CGGGTGTGGAGCTTTTCAGAT 60.612 52.381 0.00 0.00 0.00 2.90
695 776 2.519013 GGGTGTGGAGCTTTTCAGATT 58.481 47.619 0.00 0.00 0.00 2.40
696 777 2.893489 GGGTGTGGAGCTTTTCAGATTT 59.107 45.455 0.00 0.00 0.00 2.17
697 778 4.079253 GGGTGTGGAGCTTTTCAGATTTA 58.921 43.478 0.00 0.00 0.00 1.40
698 779 4.706962 GGGTGTGGAGCTTTTCAGATTTAT 59.293 41.667 0.00 0.00 0.00 1.40
699 780 5.185828 GGGTGTGGAGCTTTTCAGATTTATT 59.814 40.000 0.00 0.00 0.00 1.40
700 781 6.295292 GGGTGTGGAGCTTTTCAGATTTATTT 60.295 38.462 0.00 0.00 0.00 1.40
701 782 7.093945 GGGTGTGGAGCTTTTCAGATTTATTTA 60.094 37.037 0.00 0.00 0.00 1.40
702 783 7.755373 GGTGTGGAGCTTTTCAGATTTATTTAC 59.245 37.037 0.00 0.00 0.00 2.01
703 784 8.515414 GTGTGGAGCTTTTCAGATTTATTTACT 58.485 33.333 0.00 0.00 0.00 2.24
704 785 9.077885 TGTGGAGCTTTTCAGATTTATTTACTT 57.922 29.630 0.00 0.00 0.00 2.24
705 786 9.914131 GTGGAGCTTTTCAGATTTATTTACTTT 57.086 29.630 0.00 0.00 0.00 2.66
714 795 9.897744 TTCAGATTTATTTACTTTTGACTGCTG 57.102 29.630 0.00 0.00 0.00 4.41
715 796 8.023128 TCAGATTTATTTACTTTTGACTGCTGC 58.977 33.333 0.00 0.00 0.00 5.25
716 797 8.025445 CAGATTTATTTACTTTTGACTGCTGCT 58.975 33.333 0.00 0.00 0.00 4.24
717 798 8.239998 AGATTTATTTACTTTTGACTGCTGCTC 58.760 33.333 0.00 0.00 0.00 4.26
718 799 3.878086 TTTACTTTTGACTGCTGCTCG 57.122 42.857 0.00 0.00 0.00 5.03
719 800 1.795768 TACTTTTGACTGCTGCTCGG 58.204 50.000 0.00 0.00 0.00 4.63
720 801 0.179045 ACTTTTGACTGCTGCTCGGT 60.179 50.000 0.00 0.00 36.89 4.69
721 802 0.947244 CTTTTGACTGCTGCTCGGTT 59.053 50.000 0.00 0.00 33.57 4.44
722 803 1.334869 CTTTTGACTGCTGCTCGGTTT 59.665 47.619 0.00 0.00 33.57 3.27
723 804 2.248280 TTTGACTGCTGCTCGGTTTA 57.752 45.000 0.00 0.00 33.57 2.01
724 805 2.472695 TTGACTGCTGCTCGGTTTAT 57.527 45.000 0.00 0.00 33.57 1.40
725 806 3.603158 TTGACTGCTGCTCGGTTTATA 57.397 42.857 0.00 0.00 33.57 0.98
726 807 3.603158 TGACTGCTGCTCGGTTTATAA 57.397 42.857 0.00 0.00 33.57 0.98
727 808 3.521560 TGACTGCTGCTCGGTTTATAAG 58.478 45.455 0.00 0.00 33.57 1.73
728 809 2.280628 ACTGCTGCTCGGTTTATAAGC 58.719 47.619 0.00 0.00 36.56 3.09
729 810 2.279741 CTGCTGCTCGGTTTATAAGCA 58.720 47.619 0.00 0.00 43.40 3.91
730 811 2.874701 CTGCTGCTCGGTTTATAAGCAT 59.125 45.455 0.00 0.00 44.44 3.79
731 812 2.872245 TGCTGCTCGGTTTATAAGCATC 59.128 45.455 0.00 0.00 44.44 3.91
732 813 3.134458 GCTGCTCGGTTTATAAGCATCT 58.866 45.455 1.55 0.00 44.44 2.90
733 814 3.561725 GCTGCTCGGTTTATAAGCATCTT 59.438 43.478 1.55 0.00 44.44 2.40
734 815 4.035675 GCTGCTCGGTTTATAAGCATCTTT 59.964 41.667 1.55 0.00 44.44 2.52
735 816 5.484173 TGCTCGGTTTATAAGCATCTTTG 57.516 39.130 1.55 0.00 40.91 2.77
736 817 4.335315 TGCTCGGTTTATAAGCATCTTTGG 59.665 41.667 1.55 0.00 40.91 3.28
737 818 4.574828 GCTCGGTTTATAAGCATCTTTGGA 59.425 41.667 1.55 0.00 36.06 3.53
738 819 5.504173 GCTCGGTTTATAAGCATCTTTGGAC 60.504 44.000 1.55 0.00 36.06 4.02
739 820 4.879545 TCGGTTTATAAGCATCTTTGGACC 59.120 41.667 1.55 0.00 0.00 4.46
740 821 4.881850 CGGTTTATAAGCATCTTTGGACCT 59.118 41.667 1.55 0.00 0.00 3.85
741 822 5.357032 CGGTTTATAAGCATCTTTGGACCTT 59.643 40.000 1.55 0.00 0.00 3.50
742 823 6.540914 CGGTTTATAAGCATCTTTGGACCTTA 59.459 38.462 1.55 0.00 0.00 2.69
743 824 7.228706 CGGTTTATAAGCATCTTTGGACCTTAT 59.771 37.037 1.55 0.00 35.47 1.73
744 825 9.569122 GGTTTATAAGCATCTTTGGACCTTATA 57.431 33.333 1.55 0.00 34.33 0.98
747 828 9.569122 TTATAAGCATCTTTGGACCTTATAACC 57.431 33.333 0.00 0.00 37.09 2.85
748 829 5.717119 AGCATCTTTGGACCTTATAACCT 57.283 39.130 0.00 0.00 0.00 3.50
749 830 6.079712 AGCATCTTTGGACCTTATAACCTT 57.920 37.500 0.00 0.00 0.00 3.50
750 831 5.888161 AGCATCTTTGGACCTTATAACCTTG 59.112 40.000 0.00 0.00 0.00 3.61
751 832 5.652452 GCATCTTTGGACCTTATAACCTTGT 59.348 40.000 0.00 0.00 0.00 3.16
752 833 6.152831 GCATCTTTGGACCTTATAACCTTGTT 59.847 38.462 0.00 0.00 0.00 2.83
753 834 7.338449 GCATCTTTGGACCTTATAACCTTGTTA 59.662 37.037 0.00 0.00 0.00 2.41
754 835 8.674607 CATCTTTGGACCTTATAACCTTGTTAC 58.325 37.037 0.00 0.00 0.00 2.50
755 836 6.875195 TCTTTGGACCTTATAACCTTGTTACG 59.125 38.462 0.00 0.00 0.00 3.18
756 837 5.743636 TGGACCTTATAACCTTGTTACGT 57.256 39.130 0.00 0.00 0.00 3.57
757 838 6.112927 TGGACCTTATAACCTTGTTACGTT 57.887 37.500 0.00 0.00 0.00 3.99
758 839 6.532826 TGGACCTTATAACCTTGTTACGTTT 58.467 36.000 0.00 0.00 0.00 3.60
759 840 6.997476 TGGACCTTATAACCTTGTTACGTTTT 59.003 34.615 0.00 0.00 0.00 2.43
760 841 7.501892 TGGACCTTATAACCTTGTTACGTTTTT 59.498 33.333 0.00 0.00 0.00 1.94
761 842 8.998377 GGACCTTATAACCTTGTTACGTTTTTA 58.002 33.333 0.00 0.00 0.00 1.52
783 864 9.993454 TTTTATTTAATAATATGGCTGCATGCA 57.007 25.926 21.29 21.29 45.15 3.96
786 867 7.892778 TTTAATAATATGGCTGCATGCATTG 57.107 32.000 22.97 12.00 45.15 2.82
787 868 5.731957 AATAATATGGCTGCATGCATTGA 57.268 34.783 22.97 8.02 45.15 2.57
788 869 5.932619 ATAATATGGCTGCATGCATTGAT 57.067 34.783 22.97 14.80 45.15 2.57
789 870 4.617253 AATATGGCTGCATGCATTGATT 57.383 36.364 22.97 13.22 45.15 2.57
790 871 5.731957 AATATGGCTGCATGCATTGATTA 57.268 34.783 22.97 10.07 45.15 1.75
791 872 5.731957 ATATGGCTGCATGCATTGATTAA 57.268 34.783 22.97 4.32 45.15 1.40
792 873 4.617253 ATGGCTGCATGCATTGATTAAT 57.383 36.364 22.97 5.65 45.15 1.40
793 874 3.723260 TGGCTGCATGCATTGATTAATG 58.277 40.909 22.97 7.15 45.17 1.90
802 883 3.278367 CATTGATTAATGCAGAGGCCG 57.722 47.619 0.00 0.00 37.47 6.13
803 884 1.679139 TTGATTAATGCAGAGGCCGG 58.321 50.000 0.00 0.00 40.13 6.13
804 885 0.179020 TGATTAATGCAGAGGCCGGG 60.179 55.000 2.18 0.00 40.13 5.73
805 886 0.890996 GATTAATGCAGAGGCCGGGG 60.891 60.000 2.18 0.00 40.13 5.73
806 887 2.357593 ATTAATGCAGAGGCCGGGGG 62.358 60.000 2.18 0.00 40.13 5.40
810 891 4.678743 GCAGAGGCCGGGGGTTTT 62.679 66.667 2.18 0.00 0.00 2.43
811 892 2.117423 CAGAGGCCGGGGGTTTTT 59.883 61.111 2.18 0.00 0.00 1.94
812 893 1.977009 CAGAGGCCGGGGGTTTTTC 60.977 63.158 2.18 0.00 0.00 2.29
813 894 2.160853 AGAGGCCGGGGGTTTTTCT 61.161 57.895 2.18 0.00 0.00 2.52
814 895 1.228769 GAGGCCGGGGGTTTTTCTT 60.229 57.895 2.18 0.00 0.00 2.52
815 896 0.830444 GAGGCCGGGGGTTTTTCTTT 60.830 55.000 2.18 0.00 0.00 2.52
816 897 0.399376 AGGCCGGGGGTTTTTCTTTT 60.399 50.000 2.18 0.00 0.00 2.27
817 898 0.034337 GGCCGGGGGTTTTTCTTTTC 59.966 55.000 2.18 0.00 0.00 2.29
818 899 1.045407 GCCGGGGGTTTTTCTTTTCT 58.955 50.000 2.18 0.00 0.00 2.52
819 900 1.414919 GCCGGGGGTTTTTCTTTTCTT 59.585 47.619 2.18 0.00 0.00 2.52
820 901 2.158871 GCCGGGGGTTTTTCTTTTCTTT 60.159 45.455 2.18 0.00 0.00 2.52
821 902 3.683281 GCCGGGGGTTTTTCTTTTCTTTT 60.683 43.478 2.18 0.00 0.00 2.27
822 903 4.519213 CCGGGGGTTTTTCTTTTCTTTTT 58.481 39.130 0.00 0.00 0.00 1.94
860 941 1.286354 TTTGGTTTCTAGCGGCGTCG 61.286 55.000 4.29 4.29 39.81 5.12
865 946 1.019673 TTTCTAGCGGCGTCGTAGAT 58.980 50.000 12.58 0.00 40.67 1.98
879 1895 6.681599 GGCGTCGTAGATTGAATAAAAGAAAC 59.318 38.462 0.00 0.00 40.67 2.78
917 1933 1.001158 CGCCTAGCTAGCTACAGTTCC 60.001 57.143 20.67 4.12 0.00 3.62
946 1970 7.548075 GGAACTTTCGATTACAGTAATCTCCAA 59.452 37.037 24.67 14.73 41.80 3.53
996 2020 1.153823 CGTACGGTCCCAAGCTCTG 60.154 63.158 7.57 0.00 0.00 3.35
1103 2131 5.808030 CCTCGTGATAAACTCTTTTCTCTCC 59.192 44.000 0.00 0.00 0.00 3.71
1110 2138 8.260818 TGATAAACTCTTTTCTCTCCGATTCAT 58.739 33.333 0.00 0.00 0.00 2.57
1337 2478 1.208358 CATCTTGTGCGTGCAGGTG 59.792 57.895 8.40 0.00 0.00 4.00
1425 2566 4.681978 GGGCCAGAGCAACGTCGT 62.682 66.667 4.39 0.00 42.56 4.34
1546 2687 3.063084 GTCTCCTGCTCCGTCGGT 61.063 66.667 11.88 0.00 0.00 4.69
1577 2733 2.638363 GGTTCCTTCCAACCACTCTACT 59.362 50.000 0.00 0.00 44.79 2.57
1578 2734 3.836562 GGTTCCTTCCAACCACTCTACTA 59.163 47.826 0.00 0.00 44.79 1.82
1579 2735 4.322574 GGTTCCTTCCAACCACTCTACTAC 60.323 50.000 0.00 0.00 44.79 2.73
1588 2744 4.891992 ACCACTCTACTACACAGCAATT 57.108 40.909 0.00 0.00 0.00 2.32
1602 2758 7.928307 ACACAGCAATTAATAATCACTCTGT 57.072 32.000 0.00 0.00 33.13 3.41
1620 2776 4.274147 TCTGTACCAGAGTCTGAATCTCC 58.726 47.826 22.09 3.86 35.39 3.71
1667 2823 6.759497 TCAGAATATCGTTCTGACTTCTGA 57.241 37.500 14.56 13.47 46.95 3.27
1668 2824 6.556212 TCAGAATATCGTTCTGACTTCTGAC 58.444 40.000 14.56 0.00 46.95 3.51
1669 2825 6.151144 TCAGAATATCGTTCTGACTTCTGACA 59.849 38.462 14.56 0.00 46.95 3.58
1670 2826 6.977502 CAGAATATCGTTCTGACTTCTGACAT 59.022 38.462 11.34 0.00 46.57 3.06
1671 2827 7.490725 CAGAATATCGTTCTGACTTCTGACATT 59.509 37.037 11.34 0.00 46.57 2.71
1672 2828 7.490725 AGAATATCGTTCTGACTTCTGACATTG 59.509 37.037 0.00 0.00 33.12 2.82
1845 3229 1.671850 GCAGCACTTTCAGCGTACCTA 60.672 52.381 0.00 0.00 37.01 3.08
2218 3602 2.430367 GCAGGTTTCACCGACCCT 59.570 61.111 0.00 0.00 44.90 4.34
2464 4257 0.170561 GTGCTGCTTGCTTGATCAGG 59.829 55.000 0.00 0.00 43.37 3.86
2738 4531 1.270839 CCATGTCCACCTTCGAAGTGT 60.271 52.381 23.03 17.01 33.20 3.55
2750 4543 1.358877 CGAAGTGTTCGCCATCATCA 58.641 50.000 0.00 0.00 46.97 3.07
2753 4546 0.615331 AGTGTTCGCCATCATCACCT 59.385 50.000 0.00 0.00 0.00 4.00
2755 4548 2.236146 AGTGTTCGCCATCATCACCTTA 59.764 45.455 0.00 0.00 0.00 2.69
2758 4551 3.270877 GTTCGCCATCATCACCTTAGTT 58.729 45.455 0.00 0.00 0.00 2.24
3121 4914 3.027412 TCTGAGCTCATTCCTACTGACC 58.973 50.000 18.63 0.00 0.00 4.02
3127 4920 2.163815 CTCATTCCTACTGACCGTCGTT 59.836 50.000 0.00 0.00 0.00 3.85
3128 4921 2.094906 TCATTCCTACTGACCGTCGTTG 60.095 50.000 0.00 0.00 0.00 4.10
3251 5044 3.058016 CGTGAATCTGATGGCTTTTGTGT 60.058 43.478 0.00 0.00 0.00 3.72
3337 5132 3.957586 CACCAGTCAGGCCAGGCA 61.958 66.667 15.19 0.00 43.14 4.75
3348 5143 1.228245 GCCAGGCAGACAAGTGGAA 60.228 57.895 6.55 0.00 31.04 3.53
3460 5273 0.193574 ACCTTCTCCCCCAAGTCTCA 59.806 55.000 0.00 0.00 0.00 3.27
3466 5279 1.137872 CTCCCCCAAGTCTCAATCTCG 59.862 57.143 0.00 0.00 0.00 4.04
3574 5398 2.801631 GCCCCTCACATCCTCTCGG 61.802 68.421 0.00 0.00 0.00 4.63
3582 5406 2.060383 CATCCTCTCGGTCCAGCCA 61.060 63.158 0.00 0.00 36.97 4.75
3787 5611 1.148759 GAAGCGCTTCGATGAGACCC 61.149 60.000 32.36 8.37 0.00 4.46
3853 5677 1.067060 CGCAAGTATCCACGGATCTGA 59.933 52.381 9.00 0.00 36.17 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.813610 CCACTGACTTGTCGCCAACA 60.814 55.000 0.00 0.00 35.59 3.33
137 141 7.505585 TGAGTTTCCTTTGTCAATTCATAGGTT 59.494 33.333 1.14 0.00 37.64 3.50
146 150 4.956075 ACCTTGTGAGTTTCCTTTGTCAAT 59.044 37.500 0.00 0.00 0.00 2.57
281 288 6.055588 TGAGTATGGCTAAAATAGTTCAGGC 58.944 40.000 0.00 0.00 0.00 4.85
460 467 7.120579 TGTCACGGCTTCTATAAATGTCATTTT 59.879 33.333 15.77 7.06 33.82 1.82
477 555 8.519526 TGATTTTTATTTATCTTTGTCACGGCT 58.480 29.630 0.00 0.00 0.00 5.52
478 556 8.682128 TGATTTTTATTTATCTTTGTCACGGC 57.318 30.769 0.00 0.00 0.00 5.68
517 595 8.899427 TCATCACTCCAAAATGCATTTAAAAA 57.101 26.923 24.35 10.02 0.00 1.94
518 596 9.504708 AATCATCACTCCAAAATGCATTTAAAA 57.495 25.926 24.35 11.65 0.00 1.52
519 597 9.504708 AAATCATCACTCCAAAATGCATTTAAA 57.495 25.926 24.35 11.98 0.00 1.52
520 598 9.504708 AAAATCATCACTCCAAAATGCATTTAA 57.495 25.926 24.35 12.31 0.00 1.52
521 599 9.504708 AAAAATCATCACTCCAAAATGCATTTA 57.495 25.926 24.35 8.89 0.00 1.40
522 600 7.989416 AAAATCATCACTCCAAAATGCATTT 57.011 28.000 18.99 18.99 0.00 2.32
523 601 7.989416 AAAAATCATCACTCCAAAATGCATT 57.011 28.000 5.99 5.99 0.00 3.56
554 632 4.895668 ATGAAATGGCATTTGTGGAAGT 57.104 36.364 28.78 3.16 31.47 3.01
667 748 3.461773 CTCCACACCCGGCGATCT 61.462 66.667 9.30 0.00 0.00 2.75
672 753 2.597510 AAAAGCTCCACACCCGGC 60.598 61.111 0.00 0.00 0.00 6.13
673 754 1.228124 TGAAAAGCTCCACACCCGG 60.228 57.895 0.00 0.00 0.00 5.73
675 756 2.206576 ATCTGAAAAGCTCCACACCC 57.793 50.000 0.00 0.00 0.00 4.61
676 757 5.904362 ATAAATCTGAAAAGCTCCACACC 57.096 39.130 0.00 0.00 0.00 4.16
677 758 8.515414 AGTAAATAAATCTGAAAAGCTCCACAC 58.485 33.333 0.00 0.00 0.00 3.82
678 759 8.635765 AGTAAATAAATCTGAAAAGCTCCACA 57.364 30.769 0.00 0.00 0.00 4.17
679 760 9.914131 AAAGTAAATAAATCTGAAAAGCTCCAC 57.086 29.630 0.00 0.00 0.00 4.02
688 769 9.897744 CAGCAGTCAAAAGTAAATAAATCTGAA 57.102 29.630 0.00 0.00 0.00 3.02
689 770 8.023128 GCAGCAGTCAAAAGTAAATAAATCTGA 58.977 33.333 0.00 0.00 0.00 3.27
690 771 8.025445 AGCAGCAGTCAAAAGTAAATAAATCTG 58.975 33.333 0.00 0.00 0.00 2.90
691 772 8.115490 AGCAGCAGTCAAAAGTAAATAAATCT 57.885 30.769 0.00 0.00 0.00 2.40
692 773 7.217070 CGAGCAGCAGTCAAAAGTAAATAAATC 59.783 37.037 0.00 0.00 0.00 2.17
693 774 7.023575 CGAGCAGCAGTCAAAAGTAAATAAAT 58.976 34.615 0.00 0.00 0.00 1.40
694 775 6.370593 CGAGCAGCAGTCAAAAGTAAATAAA 58.629 36.000 0.00 0.00 0.00 1.40
695 776 5.106712 CCGAGCAGCAGTCAAAAGTAAATAA 60.107 40.000 0.00 0.00 0.00 1.40
696 777 4.391830 CCGAGCAGCAGTCAAAAGTAAATA 59.608 41.667 0.00 0.00 0.00 1.40
697 778 3.189287 CCGAGCAGCAGTCAAAAGTAAAT 59.811 43.478 0.00 0.00 0.00 1.40
698 779 2.548057 CCGAGCAGCAGTCAAAAGTAAA 59.452 45.455 0.00 0.00 0.00 2.01
699 780 2.143122 CCGAGCAGCAGTCAAAAGTAA 58.857 47.619 0.00 0.00 0.00 2.24
700 781 1.070134 ACCGAGCAGCAGTCAAAAGTA 59.930 47.619 0.00 0.00 0.00 2.24
701 782 0.179045 ACCGAGCAGCAGTCAAAAGT 60.179 50.000 0.00 0.00 0.00 2.66
702 783 0.947244 AACCGAGCAGCAGTCAAAAG 59.053 50.000 0.00 0.00 0.00 2.27
703 784 1.388547 AAACCGAGCAGCAGTCAAAA 58.611 45.000 0.00 0.00 0.00 2.44
704 785 2.248280 TAAACCGAGCAGCAGTCAAA 57.752 45.000 0.00 0.00 0.00 2.69
705 786 2.472695 ATAAACCGAGCAGCAGTCAA 57.527 45.000 0.00 0.00 0.00 3.18
706 787 3.521560 CTTATAAACCGAGCAGCAGTCA 58.478 45.455 0.00 0.00 0.00 3.41
707 788 2.285488 GCTTATAAACCGAGCAGCAGTC 59.715 50.000 0.00 0.00 36.45 3.51
708 789 2.280628 GCTTATAAACCGAGCAGCAGT 58.719 47.619 0.00 0.00 36.45 4.40
709 790 2.279741 TGCTTATAAACCGAGCAGCAG 58.720 47.619 0.00 0.00 41.15 4.24
710 791 2.394930 TGCTTATAAACCGAGCAGCA 57.605 45.000 0.00 0.00 41.15 4.41
714 795 4.574828 TCCAAAGATGCTTATAAACCGAGC 59.425 41.667 0.00 0.00 36.95 5.03
715 796 5.007724 GGTCCAAAGATGCTTATAAACCGAG 59.992 44.000 0.00 0.00 0.00 4.63
716 797 4.879545 GGTCCAAAGATGCTTATAAACCGA 59.120 41.667 0.00 0.00 0.00 4.69
717 798 4.881850 AGGTCCAAAGATGCTTATAAACCG 59.118 41.667 0.00 0.00 0.00 4.44
718 799 6.775594 AAGGTCCAAAGATGCTTATAAACC 57.224 37.500 0.00 0.00 0.00 3.27
721 802 9.569122 GGTTATAAGGTCCAAAGATGCTTATAA 57.431 33.333 0.00 0.00 33.71 0.98
722 803 8.945193 AGGTTATAAGGTCCAAAGATGCTTATA 58.055 33.333 0.00 0.00 0.00 0.98
723 804 7.816411 AGGTTATAAGGTCCAAAGATGCTTAT 58.184 34.615 0.00 0.00 0.00 1.73
724 805 7.208064 AGGTTATAAGGTCCAAAGATGCTTA 57.792 36.000 0.00 0.00 0.00 3.09
725 806 6.079712 AGGTTATAAGGTCCAAAGATGCTT 57.920 37.500 0.00 0.00 0.00 3.91
726 807 5.717119 AGGTTATAAGGTCCAAAGATGCT 57.283 39.130 0.00 0.00 0.00 3.79
727 808 5.652452 ACAAGGTTATAAGGTCCAAAGATGC 59.348 40.000 0.00 0.00 0.00 3.91
728 809 7.703058 AACAAGGTTATAAGGTCCAAAGATG 57.297 36.000 0.00 0.00 0.00 2.90
729 810 7.551617 CGTAACAAGGTTATAAGGTCCAAAGAT 59.448 37.037 0.00 0.00 0.00 2.40
730 811 6.875195 CGTAACAAGGTTATAAGGTCCAAAGA 59.125 38.462 0.00 0.00 0.00 2.52
731 812 6.652062 ACGTAACAAGGTTATAAGGTCCAAAG 59.348 38.462 0.00 0.00 0.00 2.77
732 813 6.532826 ACGTAACAAGGTTATAAGGTCCAAA 58.467 36.000 0.00 0.00 0.00 3.28
733 814 6.112927 ACGTAACAAGGTTATAAGGTCCAA 57.887 37.500 0.00 0.00 0.00 3.53
734 815 5.743636 ACGTAACAAGGTTATAAGGTCCA 57.256 39.130 0.00 0.00 0.00 4.02
735 816 7.439157 AAAACGTAACAAGGTTATAAGGTCC 57.561 36.000 0.00 0.00 0.00 4.46
757 838 9.993454 TGCATGCAGCCATATTATTAAATAAAA 57.007 25.926 18.46 0.00 44.83 1.52
760 841 9.589111 CAATGCATGCAGCCATATTATTAAATA 57.411 29.630 26.69 0.00 44.83 1.40
761 842 8.315482 TCAATGCATGCAGCCATATTATTAAAT 58.685 29.630 26.69 0.00 44.83 1.40
762 843 7.668492 TCAATGCATGCAGCCATATTATTAAA 58.332 30.769 26.69 1.35 44.83 1.52
763 844 7.229581 TCAATGCATGCAGCCATATTATTAA 57.770 32.000 26.69 0.00 44.83 1.40
764 845 6.837471 TCAATGCATGCAGCCATATTATTA 57.163 33.333 26.69 0.00 44.83 0.98
765 846 5.731957 TCAATGCATGCAGCCATATTATT 57.268 34.783 26.69 9.04 44.83 1.40
766 847 5.932619 ATCAATGCATGCAGCCATATTAT 57.067 34.783 26.69 2.26 44.83 1.28
767 848 5.731957 AATCAATGCATGCAGCCATATTA 57.268 34.783 26.69 5.69 44.83 0.98
768 849 4.617253 AATCAATGCATGCAGCCATATT 57.383 36.364 26.69 16.46 44.83 1.28
769 850 5.731957 TTAATCAATGCATGCAGCCATAT 57.268 34.783 26.69 12.49 44.83 1.78
770 851 5.474825 CATTAATCAATGCATGCAGCCATA 58.525 37.500 26.69 12.02 44.83 2.74
771 852 4.314961 CATTAATCAATGCATGCAGCCAT 58.685 39.130 26.69 13.75 44.83 4.40
772 853 3.723260 CATTAATCAATGCATGCAGCCA 58.277 40.909 26.69 11.96 44.83 4.75
782 863 2.030540 CCGGCCTCTGCATTAATCAATG 60.031 50.000 0.00 0.00 43.79 2.82
783 864 2.233271 CCGGCCTCTGCATTAATCAAT 58.767 47.619 0.00 0.00 40.13 2.57
784 865 1.679139 CCGGCCTCTGCATTAATCAA 58.321 50.000 0.00 0.00 40.13 2.57
785 866 0.179020 CCCGGCCTCTGCATTAATCA 60.179 55.000 0.00 0.00 40.13 2.57
786 867 0.890996 CCCCGGCCTCTGCATTAATC 60.891 60.000 0.00 0.00 40.13 1.75
787 868 1.151450 CCCCGGCCTCTGCATTAAT 59.849 57.895 0.00 0.00 40.13 1.40
788 869 2.595095 CCCCGGCCTCTGCATTAA 59.405 61.111 0.00 0.00 40.13 1.40
789 870 3.488569 CCCCCGGCCTCTGCATTA 61.489 66.667 0.00 0.00 40.13 1.90
793 874 4.678743 AAAACCCCCGGCCTCTGC 62.679 66.667 0.00 0.00 0.00 4.26
794 875 1.977009 GAAAAACCCCCGGCCTCTG 60.977 63.158 0.00 0.00 0.00 3.35
795 876 1.726192 AAGAAAAACCCCCGGCCTCT 61.726 55.000 0.00 0.00 0.00 3.69
796 877 0.830444 AAAGAAAAACCCCCGGCCTC 60.830 55.000 0.00 0.00 0.00 4.70
797 878 0.399376 AAAAGAAAAACCCCCGGCCT 60.399 50.000 0.00 0.00 0.00 5.19
798 879 0.034337 GAAAAGAAAAACCCCCGGCC 59.966 55.000 0.00 0.00 0.00 6.13
799 880 1.045407 AGAAAAGAAAAACCCCCGGC 58.955 50.000 0.00 0.00 0.00 6.13
800 881 3.830744 AAAGAAAAGAAAAACCCCCGG 57.169 42.857 0.00 0.00 0.00 5.73
820 901 9.810545 ACCAAAAATGAGTTCGAGATTTAAAAA 57.189 25.926 0.00 0.00 0.00 1.94
821 902 9.810545 AACCAAAAATGAGTTCGAGATTTAAAA 57.189 25.926 0.00 0.00 0.00 1.52
822 903 9.810545 AAACCAAAAATGAGTTCGAGATTTAAA 57.189 25.926 0.00 0.00 0.00 1.52
823 904 9.458374 GAAACCAAAAATGAGTTCGAGATTTAA 57.542 29.630 0.00 0.00 0.00 1.52
824 905 8.846211 AGAAACCAAAAATGAGTTCGAGATTTA 58.154 29.630 0.00 0.00 0.00 1.40
825 906 7.716612 AGAAACCAAAAATGAGTTCGAGATTT 58.283 30.769 0.00 0.00 0.00 2.17
826 907 7.277174 AGAAACCAAAAATGAGTTCGAGATT 57.723 32.000 0.00 0.00 0.00 2.40
827 908 6.884280 AGAAACCAAAAATGAGTTCGAGAT 57.116 33.333 0.00 0.00 0.00 2.75
828 909 6.073222 GCTAGAAACCAAAAATGAGTTCGAGA 60.073 38.462 0.00 0.00 0.00 4.04
829 910 6.080406 GCTAGAAACCAAAAATGAGTTCGAG 58.920 40.000 0.00 0.00 0.00 4.04
830 911 5.333798 CGCTAGAAACCAAAAATGAGTTCGA 60.334 40.000 0.00 0.00 0.00 3.71
831 912 4.846137 CGCTAGAAACCAAAAATGAGTTCG 59.154 41.667 0.00 0.00 0.00 3.95
832 913 5.154222 CCGCTAGAAACCAAAAATGAGTTC 58.846 41.667 0.00 0.00 0.00 3.01
833 914 4.558697 GCCGCTAGAAACCAAAAATGAGTT 60.559 41.667 0.00 0.00 0.00 3.01
834 915 3.057526 GCCGCTAGAAACCAAAAATGAGT 60.058 43.478 0.00 0.00 0.00 3.41
835 916 3.501950 GCCGCTAGAAACCAAAAATGAG 58.498 45.455 0.00 0.00 0.00 2.90
836 917 2.095466 CGCCGCTAGAAACCAAAAATGA 60.095 45.455 0.00 0.00 0.00 2.57
837 918 2.250188 CGCCGCTAGAAACCAAAAATG 58.750 47.619 0.00 0.00 0.00 2.32
838 919 1.883926 ACGCCGCTAGAAACCAAAAAT 59.116 42.857 0.00 0.00 0.00 1.82
844 925 0.864797 CTACGACGCCGCTAGAAACC 60.865 60.000 0.00 0.00 39.95 3.27
865 946 8.225603 AGTGAGCTCTTGTTTCTTTTATTCAA 57.774 30.769 16.19 0.00 0.00 2.69
879 1895 0.725686 CGCCAATGAGTGAGCTCTTG 59.274 55.000 16.19 10.29 42.13 3.02
917 1933 1.990563 ACTGTAATCGAAAGTTCCGCG 59.009 47.619 0.00 0.00 0.00 6.46
946 1970 1.149174 CACTTGGCAGTGGAGTGGT 59.851 57.895 8.80 0.00 46.10 4.16
970 1994 0.752054 TGGGACCGTACGACTTTTGT 59.248 50.000 18.76 4.34 0.00 2.83
1103 2131 4.717233 TCCATGGGTCAAAAATGAATCG 57.283 40.909 13.02 0.00 0.00 3.34
1110 2138 4.463539 CAGACATCATCCATGGGTCAAAAA 59.536 41.667 13.02 0.00 36.72 1.94
1337 2478 1.811679 GGCAGTAGCAGAAGTCGGC 60.812 63.158 0.00 0.00 44.61 5.54
1446 2587 2.971598 TAGCAGGTGCCCTTCCAGC 61.972 63.158 0.00 0.00 43.38 4.85
1546 2687 0.606604 GGAAGGAACCTACTGCGACA 59.393 55.000 0.00 0.00 0.00 4.35
1578 2734 7.928307 ACAGAGTGATTATTAATTGCTGTGT 57.072 32.000 13.28 13.28 33.32 3.72
1579 2735 8.338259 GGTACAGAGTGATTATTAATTGCTGTG 58.662 37.037 16.27 14.44 35.83 3.66
1602 2758 4.614475 ACATGGAGATTCAGACTCTGGTA 58.386 43.478 6.20 0.00 35.10 3.25
1620 2776 2.015588 GCTCCACTGGGACATGACATG 61.016 57.143 14.02 14.02 38.64 3.21
1845 3229 1.664965 GTTCTTGACGAGCAGCGGT 60.665 57.895 4.06 0.00 46.49 5.68
1869 3253 1.374758 GGTGAGGCCTGTGAACGAG 60.375 63.158 12.00 0.00 0.00 4.18
2347 3740 0.324943 CGGAGATCAGGGGTGTGTTT 59.675 55.000 0.00 0.00 0.00 2.83
2464 4257 1.285950 GGCGGCCTTGTCAAAGAAC 59.714 57.895 12.87 0.00 35.19 3.01
2738 4531 3.531538 GAACTAAGGTGATGATGGCGAA 58.468 45.455 0.00 0.00 0.00 4.70
2741 4534 2.213499 CGGAACTAAGGTGATGATGGC 58.787 52.381 0.00 0.00 0.00 4.40
2750 4543 1.742268 GTCGTAGAGCGGAACTAAGGT 59.258 52.381 0.00 0.00 41.72 3.50
3041 4834 2.126071 CACGGTCTTCATCGCGGT 60.126 61.111 6.13 0.00 0.00 5.68
3090 4883 1.318576 TGAGCTCAGATAATCGCCGA 58.681 50.000 13.74 0.00 0.00 5.54
3100 4893 3.027412 GGTCAGTAGGAATGAGCTCAGA 58.973 50.000 22.96 8.23 41.00 3.27
3121 4914 3.103911 GTCGCCCACTCAACGACG 61.104 66.667 0.00 0.00 45.52 5.12
3127 4920 4.034258 GTCGACGTCGCCCACTCA 62.034 66.667 32.19 11.25 39.60 3.41
3251 5044 3.473647 CCTCCTGGCGATGCAGGA 61.474 66.667 8.86 8.86 44.60 3.86
3337 5132 0.180406 AAGCCGTGTTCCACTTGTCT 59.820 50.000 0.00 0.00 31.34 3.41
3460 5273 0.691413 GAGGGGAAGGGGACGAGATT 60.691 60.000 0.00 0.00 0.00 2.40
3466 5279 3.715848 ATCGGGAGGGGAAGGGGAC 62.716 68.421 0.00 0.00 0.00 4.46
3574 5398 1.680338 GGTGGATGTTATGGCTGGAC 58.320 55.000 0.00 0.00 0.00 4.02
3582 5406 4.124910 CGCAGCGGTGGATGTTAT 57.875 55.556 17.54 0.00 0.00 1.89
3679 5503 2.282180 GGCGGAAGGTTTGCTGGA 60.282 61.111 0.00 0.00 0.00 3.86
3840 5664 1.141881 GTGCGTCAGATCCGTGGAT 59.858 57.895 0.00 0.00 37.59 3.41
3853 5677 3.425713 CTGCTTGCGGATGTGCGT 61.426 61.111 0.00 0.00 37.81 5.24


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

AutoCloner maintained by Alex Coulton.