Multiple sequence alignment - TraesCS2B01G035500

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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 TraesCS2B01G035500 chr2B 100.000 4058 0 0 1 4058 17038810 17042867 0.000000e+00 7494.0
1 TraesCS2B01G035500 chr2B 93.662 994 50 10 3071 4058 7600083 7601069 0.000000e+00 1474.0
2 TraesCS2B01G035500 chr2B 91.429 210 11 6 2658 2862 659871128 659870921 8.590000e-72 281.0
3 TraesCS2B01G035500 chr5B 96.935 1664 44 7 2396 4058 72035526 72033869 0.000000e+00 2784.0
4 TraesCS2B01G035500 chr5B 95.027 1126 29 7 2396 3521 14532297 14533395 0.000000e+00 1744.0
5 TraesCS2B01G035500 chr5B 92.683 1148 74 10 2916 4058 711516144 711515002 0.000000e+00 1646.0
6 TraesCS2B01G035500 chr7B 96.755 1664 50 3 2396 4058 432725042 432723382 0.000000e+00 2771.0
7 TraesCS2B01G035500 chr7B 92.348 1150 75 13 2916 4058 20986611 20985468 0.000000e+00 1624.0
8 TraesCS2B01G035500 chr7B 93.164 1024 64 6 3036 4058 256973312 256974330 0.000000e+00 1498.0
9 TraesCS2B01G035500 chr7B 96.809 94 3 0 908 1001 432726628 432726535 1.510000e-34 158.0
10 TraesCS2B01G035500 chr7B 84.615 78 12 0 1477 1554 265430596 265430673 1.210000e-10 78.7
11 TraesCS2B01G035500 chr7B 97.297 37 1 0 910 946 475103511 475103547 3.390000e-06 63.9
12 TraesCS2B01G035500 chr4B 94.460 1390 49 13 1009 2395 23822662 23821298 0.000000e+00 2115.0
13 TraesCS2B01G035500 chr4B 91.463 1148 85 11 2916 4058 233160808 233159669 0.000000e+00 1565.0
14 TraesCS2B01G035500 chr4B 90.010 1031 89 13 3036 4058 513877315 513876291 0.000000e+00 1321.0
15 TraesCS2B01G035500 chr4B 91.098 865 71 4 2396 3258 465961083 465960223 0.000000e+00 1166.0
16 TraesCS2B01G035500 chr4B 86.847 593 69 8 1 587 634310077 634310666 0.000000e+00 654.0
17 TraesCS2B01G035500 chr4B 87.368 95 9 2 909 1001 458244070 458244163 5.550000e-19 106.0
18 TraesCS2B01G035500 chr4D 94.531 1225 45 7 1184 2395 13200547 13199332 0.000000e+00 1871.0
19 TraesCS2B01G035500 chr4D 91.803 122 4 2 1007 1128 13200678 13200563 9.020000e-37 165.0
20 TraesCS2B01G035500 chr1B 91.926 1028 75 7 3037 4058 303872310 303873335 0.000000e+00 1432.0
21 TraesCS2B01G035500 chr1B 87.500 472 33 9 2396 2862 72565758 72565308 4.650000e-144 521.0
22 TraesCS2B01G035500 chr1B 89.583 96 7 2 908 1001 635332203 635332297 7.130000e-23 119.0
23 TraesCS2B01G035500 chr3B 91.798 951 71 6 2396 3343 324684501 324683555 0.000000e+00 1317.0
24 TraesCS2B01G035500 chr3B 89.699 1029 90 13 3039 4058 49983023 49982002 0.000000e+00 1299.0
25 TraesCS2B01G035500 chr3B 90.706 807 70 4 2396 3200 520177544 520176741 0.000000e+00 1070.0
26 TraesCS2B01G035500 chr3B 95.745 94 3 1 908 1001 520179127 520179035 2.530000e-32 150.0
27 TraesCS2B01G035500 chr3B 93.478 92 5 1 910 1001 324686085 324685995 7.070000e-28 135.0
28 TraesCS2B01G035500 chr4A 91.473 774 38 6 1625 2395 589108605 589109353 0.000000e+00 1038.0
29 TraesCS2B01G035500 chr4A 94.502 582 22 3 1007 1588 589108041 589108612 0.000000e+00 889.0
30 TraesCS2B01G035500 chr6D 87.776 589 63 8 5 587 59090184 59090769 0.000000e+00 680.0
31 TraesCS2B01G035500 chr6D 88.987 454 35 7 2455 2904 398858549 398858991 7.670000e-152 547.0
32 TraesCS2B01G035500 chr6D 89.911 337 34 0 2396 2732 198924208 198923872 6.230000e-118 435.0
33 TraesCS2B01G035500 chr7A 87.648 591 64 8 1 584 23113734 23113146 0.000000e+00 678.0
34 TraesCS2B01G035500 chr7A 86.678 593 70 8 1 587 15122006 15122595 0.000000e+00 649.0
35 TraesCS2B01G035500 chr7A 85.333 75 11 0 1480 1554 306347940 306347866 1.210000e-10 78.7
36 TraesCS2B01G035500 chr5D 87.458 590 67 6 5 588 427150284 427150872 0.000000e+00 673.0
37 TraesCS2B01G035500 chr5D 87.436 589 68 5 5 587 487215075 487214487 0.000000e+00 673.0
38 TraesCS2B01G035500 chr5D 94.595 74 1 2 931 1001 152546920 152546993 1.190000e-20 111.0
39 TraesCS2B01G035500 chr3D 87.015 593 68 6 1 588 586894523 586895111 0.000000e+00 660.0
40 TraesCS2B01G035500 chr3D 94.521 73 2 1 931 1001 233775664 233775592 1.190000e-20 111.0
41 TraesCS2B01G035500 chr2D 87.097 589 69 6 5 587 79535568 79536155 0.000000e+00 660.0
42 TraesCS2B01G035500 chr2D 86.780 590 70 7 5 588 484075444 484074857 0.000000e+00 651.0
43 TraesCS2B01G035500 chr2D 88.791 339 14 10 2396 2732 596379686 596379370 1.060000e-105 394.0
44 TraesCS2B01G035500 chr1A 85.495 455 46 13 2455 2904 232463696 232464135 1.330000e-124 457.0
45 TraesCS2B01G035500 chr2A 96.809 94 3 0 908 1001 401637916 401638009 1.510000e-34 158.0
46 TraesCS2B01G035500 chr2A 96.809 94 3 0 908 1001 403629705 403629798 1.510000e-34 158.0
47 TraesCS2B01G035500 chr7D 85.333 75 11 0 1480 1554 272601465 272601391 1.210000e-10 78.7


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 TraesCS2B01G035500 chr2B 17038810 17042867 4057 False 7494.0 7494 100.0000 1 4058 1 chr2B.!!$F2 4057
1 TraesCS2B01G035500 chr2B 7600083 7601069 986 False 1474.0 1474 93.6620 3071 4058 1 chr2B.!!$F1 987
2 TraesCS2B01G035500 chr5B 72033869 72035526 1657 True 2784.0 2784 96.9350 2396 4058 1 chr5B.!!$R1 1662
3 TraesCS2B01G035500 chr5B 14532297 14533395 1098 False 1744.0 1744 95.0270 2396 3521 1 chr5B.!!$F1 1125
4 TraesCS2B01G035500 chr5B 711515002 711516144 1142 True 1646.0 1646 92.6830 2916 4058 1 chr5B.!!$R2 1142
5 TraesCS2B01G035500 chr7B 20985468 20986611 1143 True 1624.0 1624 92.3480 2916 4058 1 chr7B.!!$R1 1142
6 TraesCS2B01G035500 chr7B 256973312 256974330 1018 False 1498.0 1498 93.1640 3036 4058 1 chr7B.!!$F1 1022
7 TraesCS2B01G035500 chr7B 432723382 432726628 3246 True 1464.5 2771 96.7820 908 4058 2 chr7B.!!$R2 3150
8 TraesCS2B01G035500 chr4B 23821298 23822662 1364 True 2115.0 2115 94.4600 1009 2395 1 chr4B.!!$R1 1386
9 TraesCS2B01G035500 chr4B 233159669 233160808 1139 True 1565.0 1565 91.4630 2916 4058 1 chr4B.!!$R2 1142
10 TraesCS2B01G035500 chr4B 513876291 513877315 1024 True 1321.0 1321 90.0100 3036 4058 1 chr4B.!!$R4 1022
11 TraesCS2B01G035500 chr4B 465960223 465961083 860 True 1166.0 1166 91.0980 2396 3258 1 chr4B.!!$R3 862
12 TraesCS2B01G035500 chr4B 634310077 634310666 589 False 654.0 654 86.8470 1 587 1 chr4B.!!$F2 586
13 TraesCS2B01G035500 chr4D 13199332 13200678 1346 True 1018.0 1871 93.1670 1007 2395 2 chr4D.!!$R1 1388
14 TraesCS2B01G035500 chr1B 303872310 303873335 1025 False 1432.0 1432 91.9260 3037 4058 1 chr1B.!!$F1 1021
15 TraesCS2B01G035500 chr3B 49982002 49983023 1021 True 1299.0 1299 89.6990 3039 4058 1 chr3B.!!$R1 1019
16 TraesCS2B01G035500 chr3B 324683555 324686085 2530 True 726.0 1317 92.6380 910 3343 2 chr3B.!!$R2 2433
17 TraesCS2B01G035500 chr3B 520176741 520179127 2386 True 610.0 1070 93.2255 908 3200 2 chr3B.!!$R3 2292
18 TraesCS2B01G035500 chr4A 589108041 589109353 1312 False 963.5 1038 92.9875 1007 2395 2 chr4A.!!$F1 1388
19 TraesCS2B01G035500 chr6D 59090184 59090769 585 False 680.0 680 87.7760 5 587 1 chr6D.!!$F1 582
20 TraesCS2B01G035500 chr7A 23113146 23113734 588 True 678.0 678 87.6480 1 584 1 chr7A.!!$R1 583
21 TraesCS2B01G035500 chr7A 15122006 15122595 589 False 649.0 649 86.6780 1 587 1 chr7A.!!$F1 586
22 TraesCS2B01G035500 chr5D 427150284 427150872 588 False 673.0 673 87.4580 5 588 1 chr5D.!!$F2 583
23 TraesCS2B01G035500 chr5D 487214487 487215075 588 True 673.0 673 87.4360 5 587 1 chr5D.!!$R1 582
24 TraesCS2B01G035500 chr3D 586894523 586895111 588 False 660.0 660 87.0150 1 588 1 chr3D.!!$F1 587
25 TraesCS2B01G035500 chr2D 79535568 79536155 587 False 660.0 660 87.0970 5 587 1 chr2D.!!$F1 582
26 TraesCS2B01G035500 chr2D 484074857 484075444 587 True 651.0 651 86.7800 5 588 1 chr2D.!!$R1 583

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
277 286 0.108804 CGGAGCCAGAGAAAACGCTA 60.109 55.0 0.00 0.00 0.00 4.26 F
1001 1016 0.106419 GAGAAACCCACACCCACCAA 60.106 55.0 0.00 0.00 0.00 3.67 F
1002 1017 0.336737 AGAAACCCACACCCACCAAA 59.663 50.0 0.00 0.00 0.00 3.28 F
1975 2463 0.538118 CAGGCCAATTTCACCATGGG 59.462 55.0 18.09 5.22 34.71 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2908 0.462937 CGGCATCCATCAAACCGGTA 60.463 55.000 8.00 0.0 40.18 4.02 R
2598 3406 0.392863 ACAATCGCCTGCACTGCATA 60.393 50.000 3.64 0.0 38.13 3.14 R
2771 3580 8.709386 AACATACAGCAAGATGACTACTAAAG 57.291 34.615 0.00 0.0 0.00 1.85 R
3643 4470 1.329599 GTCGGACAGAAAAACGCACTT 59.670 47.619 2.62 0.0 0.00 3.16 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
24 25 2.039624 AGCCTCCCGACCACATCT 59.960 61.111 0.00 0.00 0.00 2.90
61 62 2.029073 CCAGCAAGGTCACGACGT 59.971 61.111 0.00 0.00 0.00 4.34
62 63 1.174078 TCCAGCAAGGTCACGACGTA 61.174 55.000 0.00 0.00 39.02 3.57
233 242 1.681076 GCTTCCGTTGGTCCCCTAA 59.319 57.895 0.00 0.00 0.00 2.69
256 265 2.410687 CCACCAACACGCACCAACA 61.411 57.895 0.00 0.00 0.00 3.33
271 280 0.250295 CAACACCGGAGCCAGAGAAA 60.250 55.000 9.46 0.00 0.00 2.52
273 282 0.250338 ACACCGGAGCCAGAGAAAAC 60.250 55.000 9.46 0.00 0.00 2.43
274 283 1.004918 ACCGGAGCCAGAGAAAACG 60.005 57.895 9.46 0.00 0.00 3.60
275 284 2.391389 CCGGAGCCAGAGAAAACGC 61.391 63.158 0.00 0.00 0.00 4.84
277 286 0.108804 CGGAGCCAGAGAAAACGCTA 60.109 55.000 0.00 0.00 0.00 4.26
308 321 2.104729 GCGAGAGAGAGGCAGCAG 59.895 66.667 0.00 0.00 0.00 4.24
322 336 1.892329 GCAGCAGGGAAAGGGATTTCA 60.892 52.381 3.41 0.00 32.77 2.69
324 338 3.102204 CAGCAGGGAAAGGGATTTCAAT 58.898 45.455 3.41 0.00 32.77 2.57
344 358 2.649190 TCCTCCAGATCTGACGAAGAG 58.351 52.381 24.62 19.10 38.67 2.85
345 359 1.066908 CCTCCAGATCTGACGAAGAGC 59.933 57.143 24.62 0.00 41.91 4.09
350 364 2.426738 CAGATCTGACGAAGAGCCTTCT 59.573 50.000 18.34 0.00 42.62 2.85
529 544 1.536676 CCCACCACCACCTTCACTT 59.463 57.895 0.00 0.00 0.00 3.16
534 549 1.893808 CACCACCTTCACTTGCGCT 60.894 57.895 9.73 0.00 0.00 5.92
537 552 1.447317 CCACCTTCACTTGCGCTTGT 61.447 55.000 9.73 4.25 0.00 3.16
567 582 2.435693 GGCGGCCATCTCCAGTAGT 61.436 63.158 15.62 0.00 0.00 2.73
576 591 1.379977 CTCCAGTAGTGGCGAGGGA 60.380 63.158 12.14 0.00 44.60 4.20
588 603 1.051556 GCGAGGGAAGGAAGGGAGAT 61.052 60.000 0.00 0.00 0.00 2.75
589 604 0.755686 CGAGGGAAGGAAGGGAGATG 59.244 60.000 0.00 0.00 0.00 2.90
590 605 1.886422 GAGGGAAGGAAGGGAGATGT 58.114 55.000 0.00 0.00 0.00 3.06
591 606 1.488393 GAGGGAAGGAAGGGAGATGTG 59.512 57.143 0.00 0.00 0.00 3.21
592 607 1.081174 AGGGAAGGAAGGGAGATGTGA 59.919 52.381 0.00 0.00 0.00 3.58
593 608 1.210722 GGGAAGGAAGGGAGATGTGAC 59.789 57.143 0.00 0.00 0.00 3.67
594 609 2.192263 GGAAGGAAGGGAGATGTGACT 58.808 52.381 0.00 0.00 0.00 3.41
595 610 2.573915 GGAAGGAAGGGAGATGTGACTT 59.426 50.000 0.00 0.00 0.00 3.01
596 611 3.775316 GGAAGGAAGGGAGATGTGACTTA 59.225 47.826 0.00 0.00 0.00 2.24
597 612 4.225267 GGAAGGAAGGGAGATGTGACTTAA 59.775 45.833 0.00 0.00 0.00 1.85
598 613 5.280521 GGAAGGAAGGGAGATGTGACTTAAA 60.281 44.000 0.00 0.00 0.00 1.52
599 614 5.843019 AGGAAGGGAGATGTGACTTAAAA 57.157 39.130 0.00 0.00 0.00 1.52
600 615 6.200878 AGGAAGGGAGATGTGACTTAAAAA 57.799 37.500 0.00 0.00 0.00 1.94
601 616 6.004574 AGGAAGGGAGATGTGACTTAAAAAC 58.995 40.000 0.00 0.00 0.00 2.43
602 617 5.183331 GGAAGGGAGATGTGACTTAAAAACC 59.817 44.000 0.00 0.00 0.00 3.27
603 618 4.663334 AGGGAGATGTGACTTAAAAACCC 58.337 43.478 0.00 0.00 0.00 4.11
604 619 4.105697 AGGGAGATGTGACTTAAAAACCCA 59.894 41.667 0.00 0.00 36.44 4.51
605 620 5.016831 GGGAGATGTGACTTAAAAACCCAT 58.983 41.667 0.00 0.00 34.43 4.00
606 621 6.011981 AGGGAGATGTGACTTAAAAACCCATA 60.012 38.462 0.00 0.00 36.44 2.74
607 622 6.833933 GGGAGATGTGACTTAAAAACCCATAT 59.166 38.462 0.00 0.00 34.43 1.78
608 623 7.342026 GGGAGATGTGACTTAAAAACCCATATT 59.658 37.037 0.00 0.00 34.43 1.28
609 624 8.749354 GGAGATGTGACTTAAAAACCCATATTT 58.251 33.333 0.00 0.00 0.00 1.40
610 625 9.573133 GAGATGTGACTTAAAAACCCATATTTG 57.427 33.333 0.00 0.00 0.00 2.32
611 626 8.531146 AGATGTGACTTAAAAACCCATATTTGG 58.469 33.333 0.00 0.00 43.23 3.28
612 627 7.841282 TGTGACTTAAAAACCCATATTTGGA 57.159 32.000 3.41 0.00 46.92 3.53
613 628 8.429237 TGTGACTTAAAAACCCATATTTGGAT 57.571 30.769 3.41 0.00 46.92 3.41
614 629 8.310382 TGTGACTTAAAAACCCATATTTGGATG 58.690 33.333 3.41 0.00 46.92 3.51
615 630 8.311109 GTGACTTAAAAACCCATATTTGGATGT 58.689 33.333 3.41 0.00 46.92 3.06
616 631 8.310382 TGACTTAAAAACCCATATTTGGATGTG 58.690 33.333 3.41 0.00 46.92 3.21
617 632 8.429237 ACTTAAAAACCCATATTTGGATGTGA 57.571 30.769 3.41 0.00 46.92 3.58
618 633 8.311109 ACTTAAAAACCCATATTTGGATGTGAC 58.689 33.333 3.41 0.00 46.92 3.67
619 634 6.933514 AAAAACCCATATTTGGATGTGACT 57.066 33.333 3.41 0.00 46.92 3.41
620 635 9.535170 TTAAAAACCCATATTTGGATGTGACTA 57.465 29.630 3.41 0.00 46.92 2.59
621 636 8.429237 AAAAACCCATATTTGGATGTGACTAA 57.571 30.769 3.41 0.00 46.92 2.24
622 637 8.429237 AAAACCCATATTTGGATGTGACTAAA 57.571 30.769 3.41 0.00 46.92 1.85
623 638 8.608185 AAACCCATATTTGGATGTGACTAAAT 57.392 30.769 3.41 0.00 46.92 1.40
624 639 9.707957 AAACCCATATTTGGATGTGACTAAATA 57.292 29.630 3.41 0.00 46.92 1.40
625 640 9.707957 AACCCATATTTGGATGTGACTAAATAA 57.292 29.630 3.41 0.00 46.92 1.40
626 641 9.707957 ACCCATATTTGGATGTGACTAAATAAA 57.292 29.630 3.41 0.00 46.92 1.40
628 643 9.683069 CCATATTTGGATGTGACTAAATAAAGC 57.317 33.333 0.00 0.00 46.92 3.51
631 646 6.662414 TTGGATGTGACTAAATAAAGCTCG 57.338 37.500 0.00 0.00 0.00 5.03
632 647 5.116180 TGGATGTGACTAAATAAAGCTCGG 58.884 41.667 0.00 0.00 0.00 4.63
633 648 5.105106 TGGATGTGACTAAATAAAGCTCGGA 60.105 40.000 0.00 0.00 0.00 4.55
634 649 5.992217 GGATGTGACTAAATAAAGCTCGGAT 59.008 40.000 0.00 0.00 0.00 4.18
635 650 6.483640 GGATGTGACTAAATAAAGCTCGGATT 59.516 38.462 0.00 0.00 0.00 3.01
636 651 7.012421 GGATGTGACTAAATAAAGCTCGGATTT 59.988 37.037 0.00 0.00 0.00 2.17
637 652 7.681939 TGTGACTAAATAAAGCTCGGATTTT 57.318 32.000 5.94 0.00 0.00 1.82
638 653 8.106247 TGTGACTAAATAAAGCTCGGATTTTT 57.894 30.769 5.94 0.00 0.00 1.94
663 678 9.921637 TTTCATGGTGATCAAAATAAAACTACC 57.078 29.630 0.00 0.00 0.00 3.18
664 679 8.642935 TCATGGTGATCAAAATAAAACTACCA 57.357 30.769 0.00 0.00 39.68 3.25
665 680 9.253832 TCATGGTGATCAAAATAAAACTACCAT 57.746 29.630 0.00 0.00 44.65 3.55
667 682 8.642935 TGGTGATCAAAATAAAACTACCATGA 57.357 30.769 0.00 0.00 31.31 3.07
668 683 9.253832 TGGTGATCAAAATAAAACTACCATGAT 57.746 29.630 0.00 0.00 31.31 2.45
669 684 9.520204 GGTGATCAAAATAAAACTACCATGATG 57.480 33.333 0.00 0.00 0.00 3.07
727 742 9.889128 ACTAATTTCCCATGGAATAAACATTTG 57.111 29.630 15.22 6.81 41.71 2.32
730 745 9.804977 AATTTCCCATGGAATAAACATTTGAAA 57.195 25.926 15.22 9.87 41.71 2.69
731 746 9.804977 ATTTCCCATGGAATAAACATTTGAAAA 57.195 25.926 15.22 0.00 41.71 2.29
732 747 9.632638 TTTCCCATGGAATAAACATTTGAAAAA 57.367 25.926 15.22 0.00 41.71 1.94
733 748 9.804977 TTCCCATGGAATAAACATTTGAAAAAT 57.195 25.926 15.22 0.00 36.71 1.82
734 749 9.804977 TCCCATGGAATAAACATTTGAAAAATT 57.195 25.926 15.22 0.00 0.00 1.82
735 750 9.843334 CCCATGGAATAAACATTTGAAAAATTG 57.157 29.630 15.22 0.00 0.00 2.32
742 757 9.513727 AATAAACATTTGAAAAATTGTTGTGGC 57.486 25.926 0.00 0.00 0.00 5.01
743 758 6.506500 AACATTTGAAAAATTGTTGTGGCA 57.493 29.167 0.00 0.00 0.00 4.92
744 759 6.121613 ACATTTGAAAAATTGTTGTGGCAG 57.878 33.333 0.00 0.00 0.00 4.85
745 760 5.879223 ACATTTGAAAAATTGTTGTGGCAGA 59.121 32.000 0.00 0.00 0.00 4.26
746 761 6.543100 ACATTTGAAAAATTGTTGTGGCAGAT 59.457 30.769 0.00 0.00 0.00 2.90
747 762 6.601741 TTTGAAAAATTGTTGTGGCAGATC 57.398 33.333 0.00 0.00 0.00 2.75
748 763 5.273674 TGAAAAATTGTTGTGGCAGATCA 57.726 34.783 0.00 0.00 0.00 2.92
749 764 5.668471 TGAAAAATTGTTGTGGCAGATCAA 58.332 33.333 10.13 10.13 0.00 2.57
750 765 6.111382 TGAAAAATTGTTGTGGCAGATCAAA 58.889 32.000 11.52 0.00 0.00 2.69
751 766 5.989551 AAAATTGTTGTGGCAGATCAAAC 57.010 34.783 11.52 2.00 0.00 2.93
752 767 4.669206 AATTGTTGTGGCAGATCAAACA 57.331 36.364 11.52 4.34 0.00 2.83
753 768 3.435105 TTGTTGTGGCAGATCAAACAC 57.565 42.857 5.74 1.02 0.00 3.32
754 769 2.653726 TGTTGTGGCAGATCAAACACT 58.346 42.857 12.72 0.00 35.02 3.55
755 770 2.358582 TGTTGTGGCAGATCAAACACTG 59.641 45.455 12.72 0.00 35.02 3.66
767 782 8.752766 CAGATCAAACACTGCTTTTTATCATT 57.247 30.769 0.00 0.00 0.00 2.57
768 783 9.199982 CAGATCAAACACTGCTTTTTATCATTT 57.800 29.630 0.00 0.00 0.00 2.32
769 784 9.768662 AGATCAAACACTGCTTTTTATCATTTT 57.231 25.926 0.00 0.00 0.00 1.82
797 812 4.759516 AAAAATTTACCATCGCAGACGT 57.240 36.364 0.00 0.00 42.51 4.34
798 813 5.866335 AAAAATTTACCATCGCAGACGTA 57.134 34.783 0.00 0.00 42.51 3.57
799 814 6.431198 AAAAATTTACCATCGCAGACGTAT 57.569 33.333 0.00 0.00 42.51 3.06
800 815 7.542534 AAAAATTTACCATCGCAGACGTATA 57.457 32.000 0.00 0.00 42.51 1.47
801 816 7.724305 AAAATTTACCATCGCAGACGTATAT 57.276 32.000 0.00 0.00 42.51 0.86
802 817 8.821147 AAAATTTACCATCGCAGACGTATATA 57.179 30.769 0.00 0.00 42.51 0.86
803 818 8.821147 AAATTTACCATCGCAGACGTATATAA 57.179 30.769 0.00 0.00 42.51 0.98
804 819 8.821147 AATTTACCATCGCAGACGTATATAAA 57.179 30.769 0.00 0.00 42.51 1.40
805 820 8.821147 ATTTACCATCGCAGACGTATATAAAA 57.179 30.769 0.00 0.00 42.51 1.52
806 821 8.645730 TTTACCATCGCAGACGTATATAAAAA 57.354 30.769 0.00 0.00 42.51 1.94
807 822 8.821147 TTACCATCGCAGACGTATATAAAAAT 57.179 30.769 0.00 0.00 42.51 1.82
808 823 7.724305 ACCATCGCAGACGTATATAAAAATT 57.276 32.000 0.00 0.00 42.51 1.82
809 824 8.149973 ACCATCGCAGACGTATATAAAAATTT 57.850 30.769 0.00 0.00 42.51 1.82
810 825 8.067784 ACCATCGCAGACGTATATAAAAATTTG 58.932 33.333 0.00 0.00 42.51 2.32
811 826 7.059488 CCATCGCAGACGTATATAAAAATTTGC 59.941 37.037 0.00 0.00 42.51 3.68
812 827 6.423862 TCGCAGACGTATATAAAAATTTGCC 58.576 36.000 0.00 0.00 41.18 4.52
813 828 6.037281 TCGCAGACGTATATAAAAATTTGCCA 59.963 34.615 0.00 0.00 41.18 4.92
814 829 6.855914 CGCAGACGTATATAAAAATTTGCCAT 59.144 34.615 0.00 0.00 33.53 4.40
815 830 7.149144 CGCAGACGTATATAAAAATTTGCCATG 60.149 37.037 0.00 0.00 33.53 3.66
816 831 7.860373 GCAGACGTATATAAAAATTTGCCATGA 59.140 33.333 0.00 0.00 0.00 3.07
817 832 9.897744 CAGACGTATATAAAAATTTGCCATGAT 57.102 29.630 0.00 0.00 0.00 2.45
863 878 8.845413 TGCTTTGTATAAGAAATTTGGCATTT 57.155 26.923 0.00 0.00 0.00 2.32
864 879 8.934825 TGCTTTGTATAAGAAATTTGGCATTTC 58.065 29.630 0.00 5.61 38.07 2.17
865 880 9.154847 GCTTTGTATAAGAAATTTGGCATTTCT 57.845 29.630 9.69 9.69 46.74 2.52
867 882 9.995003 TTTGTATAAGAAATTTGGCATTTCTGT 57.005 25.926 14.90 10.37 44.77 3.41
874 889 8.962884 AGAAATTTGGCATTTCTGTAAAAAGT 57.037 26.923 13.74 0.00 44.11 2.66
877 892 9.830975 AAATTTGGCATTTCTGTAAAAAGTAGT 57.169 25.926 0.00 0.00 0.00 2.73
895 910 9.908152 AAAAGTAGTAATTATGACAAAGTTGCC 57.092 29.630 0.00 0.00 0.00 4.52
896 911 8.630054 AAGTAGTAATTATGACAAAGTTGCCA 57.370 30.769 0.00 0.00 0.00 4.92
897 912 8.807948 AGTAGTAATTATGACAAAGTTGCCAT 57.192 30.769 0.00 0.00 35.42 4.40
898 913 8.677300 AGTAGTAATTATGACAAAGTTGCCATG 58.323 33.333 3.40 0.00 33.28 3.66
899 914 7.701539 AGTAATTATGACAAAGTTGCCATGA 57.298 32.000 3.40 0.00 33.28 3.07
900 915 8.297470 AGTAATTATGACAAAGTTGCCATGAT 57.703 30.769 3.40 0.00 33.28 2.45
901 916 9.407380 AGTAATTATGACAAAGTTGCCATGATA 57.593 29.630 3.40 0.00 33.28 2.15
903 918 8.931385 AATTATGACAAAGTTGCCATGATAAC 57.069 30.769 3.40 0.00 33.28 1.89
904 919 5.981088 ATGACAAAGTTGCCATGATAACA 57.019 34.783 12.52 0.00 29.83 2.41
905 920 5.119931 TGACAAAGTTGCCATGATAACAC 57.880 39.130 12.52 0.00 0.00 3.32
906 921 4.022416 TGACAAAGTTGCCATGATAACACC 60.022 41.667 12.52 0.00 0.00 4.16
914 929 5.654901 TGCCATGATAACACCCCTTATTA 57.345 39.130 0.00 0.00 0.00 0.98
982 997 1.497278 CACTCAACCGAACCGCATG 59.503 57.895 0.00 0.00 0.00 4.06
1001 1016 0.106419 GAGAAACCCACACCCACCAA 60.106 55.000 0.00 0.00 0.00 3.67
1002 1017 0.336737 AGAAACCCACACCCACCAAA 59.663 50.000 0.00 0.00 0.00 3.28
1003 1018 0.750249 GAAACCCACACCCACCAAAG 59.250 55.000 0.00 0.00 0.00 2.77
1004 1019 0.689412 AAACCCACACCCACCAAAGG 60.689 55.000 0.00 0.00 0.00 3.11
1368 1555 2.126307 CGAGGTCAGTGCACGGAG 60.126 66.667 20.38 10.15 0.00 4.63
1379 1566 3.716195 CACGGAGGGATGCCACCA 61.716 66.667 19.40 0.00 0.00 4.17
1464 1880 7.703197 CGATTGATTGATTGATTGGTTGATTGA 59.297 33.333 0.00 0.00 0.00 2.57
1648 2071 6.537355 TCTCTGAATTTTCTGAACTCCATGT 58.463 36.000 0.00 0.00 35.23 3.21
1693 2121 1.195674 GCGAGCTTGACAAGGAGTTTC 59.804 52.381 16.80 0.00 0.00 2.78
1715 2143 7.880160 TTCCTGAATTTTTGAGTTCTCTGAA 57.120 32.000 1.53 0.00 0.00 3.02
1960 2448 6.200854 GCCTGTTTGTTTAAATATATGCAGGC 59.799 38.462 22.80 22.80 44.28 4.85
1975 2463 0.538118 CAGGCCAATTTCACCATGGG 59.462 55.000 18.09 5.22 34.71 4.00
2116 2608 4.980805 GTGCCGTCGGTGCCTTCA 62.981 66.667 13.94 0.00 0.00 3.02
2140 2632 2.359404 GAGGACGACTCCCCCTCA 59.641 66.667 0.00 0.00 44.42 3.86
2207 2699 2.765135 CCTCAGAGGACTGTCATGTCAT 59.235 50.000 11.62 0.00 43.81 3.06
2335 3001 2.559440 CATAAGAAGAGCCTGAGCACC 58.441 52.381 0.00 0.00 43.56 5.01
2598 3406 3.224324 AGTGTGGACGAGCGTGGT 61.224 61.111 0.00 0.00 0.00 4.16
3140 3952 2.093447 AGTTTACTCGCTCAATCCCTGG 60.093 50.000 0.00 0.00 0.00 4.45
3160 3972 0.321653 GGTCCACTCGCTTGGTCAAT 60.322 55.000 2.45 0.00 37.93 2.57
3621 4448 4.207891 AGTTCACTTGACTGTCTGTTGT 57.792 40.909 9.51 0.23 0.00 3.32
3633 4460 3.794717 TGTCTGTTGTAGTGCGGTTTTA 58.205 40.909 0.00 0.00 0.00 1.52
3636 4463 3.810941 TCTGTTGTAGTGCGGTTTTAAGG 59.189 43.478 0.00 0.00 0.00 2.69
3643 4470 3.547746 AGTGCGGTTTTAAGGTTGAAGA 58.452 40.909 0.00 0.00 0.00 2.87
3686 4514 3.687200 ACGATTTTGGTGTCACGAAAAC 58.313 40.909 23.03 16.65 38.32 2.43
3694 4523 4.304110 TGGTGTCACGAAAACATAGAGTC 58.696 43.478 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.138798 GCGTCGTCAGGGAGGCTA 61.139 66.667 0.00 0.00 42.77 3.93
84 88 0.696501 AACCCTTTATCCACTGCGGT 59.303 50.000 0.00 0.00 35.57 5.68
146 154 2.765969 CTCCATGGGGGTGCAACT 59.234 61.111 13.02 0.00 38.11 3.16
148 156 1.734420 TTTCCTCCATGGGGGTGCAA 61.734 55.000 30.50 18.15 38.11 4.08
152 160 1.856873 TGCTTTCCTCCATGGGGGT 60.857 57.895 30.50 0.00 38.11 4.95
202 210 4.388499 GAAGCCTTGGCCGTCCGA 62.388 66.667 8.17 0.00 34.14 4.55
233 242 4.497984 TGCGTGTTGGTGGCCAGT 62.498 61.111 5.11 0.00 33.81 4.00
256 265 1.004918 CGTTTTCTCTGGCTCCGGT 60.005 57.895 0.00 0.00 0.00 5.28
322 336 3.636300 CTCTTCGTCAGATCTGGAGGATT 59.364 47.826 22.42 0.00 34.33 3.01
324 338 2.649190 CTCTTCGTCAGATCTGGAGGA 58.351 52.381 22.42 16.07 0.00 3.71
483 498 1.529309 GCTCCATCCCCTCTTGGAC 59.471 63.158 0.00 0.00 37.10 4.02
487 502 3.483869 GGCGCTCCATCCCCTCTT 61.484 66.667 7.64 0.00 0.00 2.85
514 529 1.525995 CGCAAGTGAAGGTGGTGGT 60.526 57.895 0.00 0.00 0.00 4.16
556 571 0.757188 CCCTCGCCACTACTGGAGAT 60.757 60.000 0.00 0.00 44.59 2.75
567 582 3.009115 CCCTTCCTTCCCTCGCCA 61.009 66.667 0.00 0.00 0.00 5.69
576 591 5.843019 TTTAAGTCACATCTCCCTTCCTT 57.157 39.130 0.00 0.00 0.00 3.36
605 620 8.826710 CGAGCTTTATTTAGTCACATCCAAATA 58.173 33.333 0.00 0.00 0.00 1.40
606 621 7.201732 CCGAGCTTTATTTAGTCACATCCAAAT 60.202 37.037 0.00 0.00 0.00 2.32
607 622 6.093495 CCGAGCTTTATTTAGTCACATCCAAA 59.907 38.462 0.00 0.00 0.00 3.28
608 623 5.584649 CCGAGCTTTATTTAGTCACATCCAA 59.415 40.000 0.00 0.00 0.00 3.53
609 624 5.105106 TCCGAGCTTTATTTAGTCACATCCA 60.105 40.000 0.00 0.00 0.00 3.41
610 625 5.357257 TCCGAGCTTTATTTAGTCACATCC 58.643 41.667 0.00 0.00 0.00 3.51
611 626 7.484035 AATCCGAGCTTTATTTAGTCACATC 57.516 36.000 0.00 0.00 0.00 3.06
612 627 7.865706 AAATCCGAGCTTTATTTAGTCACAT 57.134 32.000 0.00 0.00 0.00 3.21
613 628 7.681939 AAAATCCGAGCTTTATTTAGTCACA 57.318 32.000 0.00 0.00 0.00 3.58
637 652 9.921637 GGTAGTTTTATTTTGATCACCATGAAA 57.078 29.630 0.00 0.00 0.00 2.69
638 653 9.083422 TGGTAGTTTTATTTTGATCACCATGAA 57.917 29.630 0.00 0.00 0.00 2.57
639 654 8.642935 TGGTAGTTTTATTTTGATCACCATGA 57.357 30.769 0.00 0.00 0.00 3.07
641 656 9.253832 TCATGGTAGTTTTATTTTGATCACCAT 57.746 29.630 0.00 0.00 43.27 3.55
642 657 8.642935 TCATGGTAGTTTTATTTTGATCACCA 57.357 30.769 0.00 0.00 37.88 4.17
643 658 9.520204 CATCATGGTAGTTTTATTTTGATCACC 57.480 33.333 0.00 0.00 0.00 4.02
701 716 9.889128 CAAATGTTTATTCCATGGGAAATTAGT 57.111 29.630 13.02 1.50 45.41 2.24
704 719 9.804977 TTTCAAATGTTTATTCCATGGGAAATT 57.195 25.926 13.02 0.32 45.41 1.82
705 720 9.804977 TTTTCAAATGTTTATTCCATGGGAAAT 57.195 25.926 13.02 7.92 45.41 2.17
706 721 9.632638 TTTTTCAAATGTTTATTCCATGGGAAA 57.367 25.926 13.02 7.56 45.41 3.13
707 722 9.804977 ATTTTTCAAATGTTTATTCCATGGGAA 57.195 25.926 13.02 5.48 46.39 3.97
708 723 9.804977 AATTTTTCAAATGTTTATTCCATGGGA 57.195 25.926 13.02 2.34 0.00 4.37
709 724 9.843334 CAATTTTTCAAATGTTTATTCCATGGG 57.157 29.630 13.02 0.00 0.00 4.00
716 731 9.513727 GCCACAACAATTTTTCAAATGTTTATT 57.486 25.926 0.00 0.00 33.97 1.40
717 732 8.680903 TGCCACAACAATTTTTCAAATGTTTAT 58.319 25.926 0.00 0.00 33.97 1.40
718 733 8.044060 TGCCACAACAATTTTTCAAATGTTTA 57.956 26.923 0.00 0.00 33.97 2.01
719 734 6.917533 TGCCACAACAATTTTTCAAATGTTT 58.082 28.000 0.00 0.00 33.97 2.83
720 735 6.373774 TCTGCCACAACAATTTTTCAAATGTT 59.626 30.769 0.00 0.00 36.49 2.71
721 736 5.879223 TCTGCCACAACAATTTTTCAAATGT 59.121 32.000 0.00 0.00 0.00 2.71
722 737 6.360844 TCTGCCACAACAATTTTTCAAATG 57.639 33.333 0.00 0.00 0.00 2.32
723 738 6.766944 TGATCTGCCACAACAATTTTTCAAAT 59.233 30.769 0.00 0.00 0.00 2.32
724 739 6.111382 TGATCTGCCACAACAATTTTTCAAA 58.889 32.000 0.00 0.00 0.00 2.69
725 740 5.668471 TGATCTGCCACAACAATTTTTCAA 58.332 33.333 0.00 0.00 0.00 2.69
726 741 5.273674 TGATCTGCCACAACAATTTTTCA 57.726 34.783 0.00 0.00 0.00 2.69
727 742 6.036953 TGTTTGATCTGCCACAACAATTTTTC 59.963 34.615 0.00 0.00 0.00 2.29
728 743 5.879223 TGTTTGATCTGCCACAACAATTTTT 59.121 32.000 0.00 0.00 0.00 1.94
729 744 5.294060 GTGTTTGATCTGCCACAACAATTTT 59.706 36.000 0.00 0.00 0.00 1.82
730 745 4.810491 GTGTTTGATCTGCCACAACAATTT 59.190 37.500 0.00 0.00 0.00 1.82
731 746 4.099881 AGTGTTTGATCTGCCACAACAATT 59.900 37.500 10.41 0.00 0.00 2.32
732 747 3.638160 AGTGTTTGATCTGCCACAACAAT 59.362 39.130 10.41 0.00 0.00 2.71
733 748 3.023119 AGTGTTTGATCTGCCACAACAA 58.977 40.909 10.41 0.00 0.00 2.83
734 749 2.358582 CAGTGTTTGATCTGCCACAACA 59.641 45.455 10.41 0.00 0.00 3.33
735 750 3.004024 CAGTGTTTGATCTGCCACAAC 57.996 47.619 10.41 0.00 0.00 3.32
742 757 8.752766 AATGATAAAAAGCAGTGTTTGATCTG 57.247 30.769 0.00 0.00 35.12 2.90
743 758 9.768662 AAAATGATAAAAAGCAGTGTTTGATCT 57.231 25.926 0.00 0.00 0.00 2.75
776 791 4.759516 ACGTCTGCGATGGTAAATTTTT 57.240 36.364 0.00 0.00 42.00 1.94
777 792 7.724305 ATATACGTCTGCGATGGTAAATTTT 57.276 32.000 0.00 0.00 42.00 1.82
778 793 8.821147 TTATATACGTCTGCGATGGTAAATTT 57.179 30.769 0.00 0.00 42.00 1.82
779 794 8.821147 TTTATATACGTCTGCGATGGTAAATT 57.179 30.769 0.00 0.00 42.00 1.82
780 795 8.821147 TTTTATATACGTCTGCGATGGTAAAT 57.179 30.769 0.00 0.00 42.00 1.40
781 796 8.645730 TTTTTATATACGTCTGCGATGGTAAA 57.354 30.769 0.00 0.00 42.00 2.01
782 797 8.821147 ATTTTTATATACGTCTGCGATGGTAA 57.179 30.769 0.00 0.00 42.00 2.85
783 798 8.821147 AATTTTTATATACGTCTGCGATGGTA 57.179 30.769 0.00 0.85 42.00 3.25
784 799 7.724305 AATTTTTATATACGTCTGCGATGGT 57.276 32.000 0.00 0.00 42.00 3.55
785 800 7.059488 GCAAATTTTTATATACGTCTGCGATGG 59.941 37.037 0.00 0.00 42.00 3.51
786 801 7.059488 GGCAAATTTTTATATACGTCTGCGATG 59.941 37.037 0.00 0.00 42.00 3.84
787 802 7.075741 GGCAAATTTTTATATACGTCTGCGAT 58.924 34.615 0.00 0.00 42.00 4.58
788 803 6.037281 TGGCAAATTTTTATATACGTCTGCGA 59.963 34.615 0.00 0.00 42.00 5.10
789 804 6.195868 TGGCAAATTTTTATATACGTCTGCG 58.804 36.000 0.00 0.00 44.93 5.18
790 805 7.860373 TCATGGCAAATTTTTATATACGTCTGC 59.140 33.333 0.00 0.00 0.00 4.26
791 806 9.897744 ATCATGGCAAATTTTTATATACGTCTG 57.102 29.630 0.00 0.00 0.00 3.51
837 852 9.452287 AAATGCCAAATTTCTTATACAAAGCAT 57.548 25.926 0.00 0.00 37.65 3.79
838 853 8.845413 AAATGCCAAATTTCTTATACAAAGCA 57.155 26.923 0.00 0.00 0.00 3.91
839 854 9.154847 AGAAATGCCAAATTTCTTATACAAAGC 57.845 29.630 7.36 0.00 43.52 3.51
841 856 9.995003 ACAGAAATGCCAAATTTCTTATACAAA 57.005 25.926 9.95 0.00 43.52 2.83
848 863 9.394767 ACTTTTTACAGAAATGCCAAATTTCTT 57.605 25.926 9.95 5.94 43.52 2.52
849 864 8.962884 ACTTTTTACAGAAATGCCAAATTTCT 57.037 26.923 7.36 7.36 45.99 2.52
851 866 9.830975 ACTACTTTTTACAGAAATGCCAAATTT 57.169 25.926 0.00 0.00 0.00 1.82
869 884 9.908152 GGCAACTTTGTCATAATTACTACTTTT 57.092 29.630 0.00 0.00 31.86 2.27
870 885 9.073475 TGGCAACTTTGTCATAATTACTACTTT 57.927 29.630 0.00 0.00 37.97 2.66
871 886 8.630054 TGGCAACTTTGTCATAATTACTACTT 57.370 30.769 0.00 0.00 37.97 2.24
884 899 4.485163 GGTGTTATCATGGCAACTTTGTC 58.515 43.478 0.00 0.00 37.61 3.18
885 900 3.258123 GGGTGTTATCATGGCAACTTTGT 59.742 43.478 0.00 0.00 37.61 2.83
886 901 3.368323 GGGGTGTTATCATGGCAACTTTG 60.368 47.826 0.00 0.00 37.61 2.77
887 902 2.831526 GGGGTGTTATCATGGCAACTTT 59.168 45.455 0.00 0.00 37.61 2.66
888 903 2.042979 AGGGGTGTTATCATGGCAACTT 59.957 45.455 0.00 0.00 37.61 2.66
889 904 1.640670 AGGGGTGTTATCATGGCAACT 59.359 47.619 0.00 0.00 37.61 3.16
890 905 2.143876 AGGGGTGTTATCATGGCAAC 57.856 50.000 0.00 0.00 0.00 4.17
891 906 2.917713 AAGGGGTGTTATCATGGCAA 57.082 45.000 0.00 0.00 0.00 4.52
892 907 4.534647 AATAAGGGGTGTTATCATGGCA 57.465 40.909 0.00 0.00 0.00 4.92
893 908 5.105756 GCATAATAAGGGGTGTTATCATGGC 60.106 44.000 0.00 0.00 0.00 4.40
894 909 6.009589 TGCATAATAAGGGGTGTTATCATGG 58.990 40.000 0.00 0.00 0.00 3.66
895 910 6.489700 TGTGCATAATAAGGGGTGTTATCATG 59.510 38.462 0.00 0.00 0.00 3.07
896 911 6.490040 GTGTGCATAATAAGGGGTGTTATCAT 59.510 38.462 0.00 0.00 0.00 2.45
897 912 5.825679 GTGTGCATAATAAGGGGTGTTATCA 59.174 40.000 0.00 0.00 0.00 2.15
898 913 5.240844 GGTGTGCATAATAAGGGGTGTTATC 59.759 44.000 0.00 0.00 0.00 1.75
899 914 5.137551 GGTGTGCATAATAAGGGGTGTTAT 58.862 41.667 0.00 0.00 0.00 1.89
900 915 4.018324 TGGTGTGCATAATAAGGGGTGTTA 60.018 41.667 0.00 0.00 0.00 2.41
901 916 3.245443 TGGTGTGCATAATAAGGGGTGTT 60.245 43.478 0.00 0.00 0.00 3.32
902 917 2.310349 TGGTGTGCATAATAAGGGGTGT 59.690 45.455 0.00 0.00 0.00 4.16
903 918 3.011566 TGGTGTGCATAATAAGGGGTG 57.988 47.619 0.00 0.00 0.00 4.61
904 919 3.748645 TTGGTGTGCATAATAAGGGGT 57.251 42.857 0.00 0.00 0.00 4.95
905 920 4.466015 ACTTTTGGTGTGCATAATAAGGGG 59.534 41.667 0.00 0.00 0.00 4.79
906 921 5.410067 CACTTTTGGTGTGCATAATAAGGG 58.590 41.667 0.00 0.00 40.79 3.95
982 997 0.106419 TTGGTGGGTGTGGGTTTCTC 60.106 55.000 0.00 0.00 0.00 2.87
1001 1016 0.252197 GGCTGTTCCGTCCATACCTT 59.748 55.000 0.00 0.00 0.00 3.50
1002 1017 1.905512 GGCTGTTCCGTCCATACCT 59.094 57.895 0.00 0.00 0.00 3.08
1003 1018 4.534401 GGCTGTTCCGTCCATACC 57.466 61.111 0.00 0.00 0.00 2.73
1368 1555 2.053865 CATGTGGTGGTGGCATCCC 61.054 63.158 0.00 0.00 0.00 3.85
1464 1880 1.676635 ATCTGCGCACCACAGCAAT 60.677 52.632 5.66 0.00 43.31 3.56
1648 2071 5.808366 AAGTTCAGACAACTCATGGAGTA 57.192 39.130 0.00 0.00 42.59 2.59
1693 2121 9.538508 AAAATTCAGAGAACTCAAAAATTCAGG 57.461 29.630 4.64 0.00 0.00 3.86
1715 2143 7.360361 CGTTCTTGTAGCTCCTGTTTAAAAAT 58.640 34.615 0.00 0.00 0.00 1.82
1720 2148 3.575256 TCCGTTCTTGTAGCTCCTGTTTA 59.425 43.478 0.00 0.00 0.00 2.01
1721 2149 2.367567 TCCGTTCTTGTAGCTCCTGTTT 59.632 45.455 0.00 0.00 0.00 2.83
1722 2150 1.968493 TCCGTTCTTGTAGCTCCTGTT 59.032 47.619 0.00 0.00 0.00 3.16
1960 2448 4.099881 CCATTACTCCCATGGTGAAATTGG 59.900 45.833 11.73 7.24 37.07 3.16
1975 2463 2.421424 CTGCTTCTGGTTGCCATTACTC 59.579 50.000 0.00 0.00 30.82 2.59
2104 2596 3.998672 TCCCGTGAAGGCACCGAC 61.999 66.667 0.00 0.00 42.09 4.79
2116 2608 2.745492 GAGTCGTCCTCGTCCCGT 60.745 66.667 0.00 0.00 38.33 5.28
2242 2908 0.462937 CGGCATCCATCAAACCGGTA 60.463 55.000 8.00 0.00 40.18 4.02
2335 3001 0.647410 GAACCACAGCGTCATGATCG 59.353 55.000 0.00 6.00 0.00 3.69
2598 3406 0.392863 ACAATCGCCTGCACTGCATA 60.393 50.000 3.64 0.00 38.13 3.14
2771 3580 8.709386 AACATACAGCAAGATGACTACTAAAG 57.291 34.615 0.00 0.00 0.00 1.85
3140 3952 2.047179 GACCAAGCGAGTGGACCC 60.047 66.667 11.42 0.00 41.65 4.46
3546 4373 4.632251 TCTCGCACAAGTTTTTGTTGTCTA 59.368 37.500 0.00 0.00 45.01 2.59
3621 4448 4.706035 TCTTCAACCTTAAAACCGCACTA 58.294 39.130 0.00 0.00 0.00 2.74
3633 4460 4.157840 AGAAAAACGCACTTCTTCAACCTT 59.842 37.500 0.00 0.00 0.00 3.50
3636 4463 4.412207 ACAGAAAAACGCACTTCTTCAAC 58.588 39.130 0.00 0.00 29.29 3.18
3643 4470 1.329599 GTCGGACAGAAAAACGCACTT 59.670 47.619 2.62 0.00 0.00 3.16
3686 4514 3.665173 GCAAAAAGCGGAGACTCTATG 57.335 47.619 1.74 0.00 0.00 2.23
3730 4559 7.540474 AGAACACACTCTCTAATTCCTTACA 57.460 36.000 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.