Multiple sequence alignment - TraesCS3A01G083000

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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 TraesCS3A01G083000 chr3A 100.000 4071 0 0 1 4071 53557099 53553029 0.000000e+00 7518.0
1 TraesCS3A01G083000 chr3A 97.688 173 4 0 504 676 89152748 89152576 8.550000e-77 298.0
2 TraesCS3A01G083000 chr3A 96.111 180 6 1 501 680 515830942 515831120 3.980000e-75 292.0
3 TraesCS3A01G083000 chr3A 76.177 361 79 7 3605 3962 486816695 486816339 2.500000e-42 183.0
4 TraesCS3A01G083000 chr3D 92.192 2062 83 32 1472 3513 42310811 42312814 0.000000e+00 2844.0
5 TraesCS3A01G083000 chr3D 95.048 626 29 2 666 1290 42302577 42303201 0.000000e+00 983.0
6 TraesCS3A01G083000 chr3D 94.336 565 29 3 3508 4071 42313265 42313827 0.000000e+00 863.0
7 TraesCS3A01G083000 chr3D 92.308 481 23 3 1 467 42302031 42302511 0.000000e+00 671.0
8 TraesCS3A01G083000 chr3D 94.366 71 4 0 1376 1446 42303344 42303414 4.300000e-20 110.0
9 TraesCS3A01G083000 chr3D 98.182 55 1 0 451 505 42302524 42302578 3.350000e-16 97.1
10 TraesCS3A01G083000 chr3B 89.903 1139 71 25 1376 2503 65549045 65547940 0.000000e+00 1426.0
11 TraesCS3A01G083000 chr3B 94.404 679 37 1 3393 4071 65542002 65541325 0.000000e+00 1042.0
12 TraesCS3A01G083000 chr3B 88.995 836 51 24 2578 3398 65547841 65547032 0.000000e+00 996.0
13 TraesCS3A01G083000 chr3B 90.566 636 56 4 641 1274 65550151 65549518 0.000000e+00 839.0
14 TraesCS3A01G083000 chr3B 95.597 318 12 2 214 530 65550531 65550215 3.630000e-140 508.0
15 TraesCS3A01G083000 chr5B 87.257 463 57 2 3492 3954 432703178 432702718 1.000000e-145 527.0
16 TraesCS3A01G083000 chr5B 98.256 172 3 0 501 672 396856756 396856585 6.610000e-78 302.0
17 TraesCS3A01G083000 chr5A 85.529 463 66 1 3489 3951 467759632 467760093 2.200000e-132 483.0
18 TraesCS3A01G083000 chr5A 96.133 181 6 1 501 680 371027841 371028021 1.110000e-75 294.0
19 TraesCS3A01G083000 chr5A 100.000 39 0 0 3993 4031 655925549 655925511 5.640000e-09 73.1
20 TraesCS3A01G083000 chr1D 84.440 482 69 5 3487 3967 119749181 119748705 1.710000e-128 470.0
21 TraesCS3A01G083000 chr5D 80.665 481 92 1 3487 3967 440348677 440348198 4.970000e-99 372.0
22 TraesCS3A01G083000 chr5D 80.932 472 83 4 3487 3955 99978465 99978932 2.310000e-97 366.0
23 TraesCS3A01G083000 chr1A 97.175 177 3 2 500 675 557104318 557104493 8.550000e-77 298.0
24 TraesCS3A01G083000 chr1A 97.143 175 5 0 497 671 33222197 33222023 3.080000e-76 296.0
25 TraesCS3A01G083000 chr4B 97.688 173 3 1 499 671 671749851 671749680 3.080000e-76 296.0
26 TraesCS3A01G083000 chr2A 97.159 176 3 2 493 667 603083622 603083448 3.080000e-76 296.0
27 TraesCS3A01G083000 chr2A 76.177 361 77 9 3606 3962 11960329 11960684 8.990000e-42 182.0
28 TraesCS3A01G083000 chr4A 97.126 174 3 2 495 667 515656096 515656268 3.980000e-75 292.0


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 TraesCS3A01G083000 chr3A 53553029 53557099 4070 True 7518.000 7518 100.00000 1 4071 1 chr3A.!!$R1 4070
1 TraesCS3A01G083000 chr3D 42310811 42313827 3016 False 1853.500 2844 93.26400 1472 4071 2 chr3D.!!$F2 2599
2 TraesCS3A01G083000 chr3D 42302031 42303414 1383 False 465.275 983 94.97600 1 1446 4 chr3D.!!$F1 1445
3 TraesCS3A01G083000 chr3B 65541325 65542002 677 True 1042.000 1042 94.40400 3393 4071 1 chr3B.!!$R1 678
4 TraesCS3A01G083000 chr3B 65547032 65550531 3499 True 942.250 1426 91.26525 214 3398 4 chr3B.!!$R2 3184

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
761 806 0.452184 CGCCTCTAAACGAGCAGAGA 59.548 55.0 11.66 0.0 40.68 3.10 F
1306 1353 0.034198 TGAACTGCGGTTGGATCGAA 59.966 50.0 17.49 0.0 35.58 3.71 F
1470 1929 0.093026 CGTTTTCGTGACCGATGAGC 59.907 55.0 0.00 0.0 43.80 4.26 F
2807 3326 0.105778 TGCCTTTTCTTTTTGCGGGG 59.894 50.0 0.00 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 2237 0.108329 GTCACGTGGGATTGGATCGT 60.108 55.000 17.00 0.0 35.12 3.73 R
2813 3332 0.038021 TGGCCTGCATACACACACAT 59.962 50.000 3.32 0.0 0.00 3.21 R
2833 3352 1.443407 CACCTCCGCCTGGATGTAG 59.557 63.158 0.00 0.0 45.33 2.74 R
3705 4682 0.840722 ACCCCCGTCAATGAGGACTT 60.841 55.000 4.32 0.0 35.63 3.01 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
28 29 4.679654 GTCAAAATAAAAAGACGCCACCAG 59.320 41.667 0.00 0.00 0.00 4.00
75 76 1.137513 CGTAAATCCTCGCCCGATTC 58.862 55.000 0.00 0.00 0.00 2.52
78 79 2.420058 AAATCCTCGCCCGATTCTTT 57.580 45.000 0.00 0.00 0.00 2.52
80 81 0.815615 ATCCTCGCCCGATTCTTTGC 60.816 55.000 0.00 0.00 0.00 3.68
110 111 0.668535 AACCGTGCTCCTTCAAAAGC 59.331 50.000 0.00 0.00 39.02 3.51
137 150 2.193536 ACGGGAGCACAAAGTTGGC 61.194 57.895 0.00 0.00 0.00 4.52
214 227 9.647797 CAATATGTAGGAACACAACTTAGTACA 57.352 33.333 0.00 0.00 38.78 2.90
398 413 5.787380 AGGGAAAATTTTGACATCAGCTTC 58.213 37.500 8.47 0.00 0.00 3.86
441 457 0.961019 GGTGCAAATCTCACAGCCAA 59.039 50.000 0.00 0.00 36.22 4.52
442 458 1.547372 GGTGCAAATCTCACAGCCAAT 59.453 47.619 0.00 0.00 36.22 3.16
517 562 1.020437 CGTACTACTCCCTCCGTTCC 58.980 60.000 0.00 0.00 0.00 3.62
518 563 1.407989 CGTACTACTCCCTCCGTTCCT 60.408 57.143 0.00 0.00 0.00 3.36
521 566 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
530 575 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
531 576 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
532 577 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
533 578 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
534 579 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
536 581 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
537 582 8.248945 CCGTTCCTAAATACTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
607 652 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
608 653 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
609 654 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
610 655 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
611 656 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
612 657 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
613 658 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
614 659 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
615 660 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
616 661 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
617 662 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
618 663 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
619 664 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
620 665 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
621 666 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
622 667 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
623 668 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
624 669 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
625 670 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
626 671 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
627 672 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
628 673 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
629 674 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
630 675 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
631 676 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
632 677 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
633 678 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
634 679 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
635 680 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
636 681 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
637 682 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
638 683 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
639 684 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
643 688 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
648 693 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
651 696 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
657 702 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
662 707 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
710 755 2.643551 AGCGAAAAACGATGGGATGAT 58.356 42.857 0.00 0.00 45.77 2.45
748 793 1.690219 CCCACTAGCCAATCGCCTCT 61.690 60.000 0.00 0.00 38.78 3.69
755 800 0.931005 GCCAATCGCCTCTAAACGAG 59.069 55.000 0.00 0.00 42.31 4.18
761 806 0.452184 CGCCTCTAAACGAGCAGAGA 59.548 55.000 11.66 0.00 40.68 3.10
910 955 4.373116 GCTCGTCCCGGCAGACAA 62.373 66.667 10.87 0.00 36.52 3.18
911 956 2.125912 CTCGTCCCGGCAGACAAG 60.126 66.667 10.87 0.00 36.52 3.16
1012 1057 5.809562 CAGAGCTAAAACATGAGGTAGTCAG 59.190 44.000 0.00 0.00 39.07 3.51
1020 1065 2.310779 TGAGGTAGTCAGCACTCCTT 57.689 50.000 0.00 0.00 33.01 3.36
1040 1085 2.866515 TCCTCCCTCCTTCTCTACTCT 58.133 52.381 0.00 0.00 0.00 3.24
1095 1140 9.398538 AGTAGTAGGATGTTGTGTTTGTTTAAA 57.601 29.630 0.00 0.00 0.00 1.52
1169 1215 6.947376 TGACAATATGATGAGGAGATCCAT 57.053 37.500 0.92 0.00 38.89 3.41
1251 1298 3.048602 CGGACTCGGTTCCACTGT 58.951 61.111 4.38 0.00 35.04 3.55
1260 1307 1.270305 CGGTTCCACTGTCTGTCATGT 60.270 52.381 0.00 0.00 0.00 3.21
1292 1339 4.235939 CGAAGATCATCGGAGATGAACT 57.764 45.455 15.47 14.89 45.12 3.01
1294 1341 3.383620 AGATCATCGGAGATGAACTGC 57.616 47.619 17.89 8.77 45.12 4.40
1300 1347 2.471255 GGAGATGAACTGCGGTTGG 58.529 57.895 17.49 0.00 35.58 3.77
1301 1348 0.036388 GGAGATGAACTGCGGTTGGA 60.036 55.000 17.49 2.02 35.58 3.53
1302 1349 1.407437 GGAGATGAACTGCGGTTGGAT 60.407 52.381 17.49 7.45 35.58 3.41
1303 1350 1.936547 GAGATGAACTGCGGTTGGATC 59.063 52.381 17.49 15.97 35.58 3.36
1304 1351 0.652592 GATGAACTGCGGTTGGATCG 59.347 55.000 17.49 0.00 35.58 3.69
1305 1352 0.249120 ATGAACTGCGGTTGGATCGA 59.751 50.000 17.49 0.00 35.58 3.59
1306 1353 0.034198 TGAACTGCGGTTGGATCGAA 59.966 50.000 17.49 0.00 35.58 3.71
1307 1354 0.721718 GAACTGCGGTTGGATCGAAG 59.278 55.000 17.49 0.00 39.10 3.79
1308 1355 1.298859 AACTGCGGTTGGATCGAAGC 61.299 55.000 10.90 9.37 36.79 3.86
1309 1356 2.802667 CTGCGGTTGGATCGAAGCG 61.803 63.158 29.91 29.91 46.86 4.68
1347 1394 5.539048 GAAAGTGAAGTGGACTAGCAAGTA 58.461 41.667 0.00 0.00 35.56 2.24
1369 1416 2.215465 TAGCGTTCCGTGCGAATGGA 62.215 55.000 0.00 0.00 37.86 3.41
1382 1841 4.022416 GTGCGAATGGAGAGAGAGATATGT 60.022 45.833 0.00 0.00 0.00 2.29
1402 1861 1.093159 GCTGAGTTTGAGGGATGCTG 58.907 55.000 0.00 0.00 0.00 4.41
1439 1898 7.503566 ACATGTATAATGATTTTCTGAGGGGTG 59.496 37.037 0.00 0.00 0.00 4.61
1466 1925 0.233848 GTTGCGTTTTCGTGACCGAT 59.766 50.000 0.00 0.00 43.80 4.18
1470 1929 0.093026 CGTTTTCGTGACCGATGAGC 59.907 55.000 0.00 0.00 43.80 4.26
1489 1948 1.067354 GCAAGGGCAGTTTGAAGGATG 60.067 52.381 0.61 0.00 40.72 3.51
1599 2058 1.153997 GAAGACGACGGAGACCAGC 60.154 63.158 0.00 0.00 0.00 4.85
1609 2068 1.374758 GAGACCAGCCACGAACCAG 60.375 63.158 0.00 0.00 0.00 4.00
1662 2121 1.718757 GGTCGTCCGGTAGCGTACAT 61.719 60.000 13.99 0.00 0.00 2.29
1663 2122 0.590732 GTCGTCCGGTAGCGTACATG 60.591 60.000 13.99 2.58 0.00 3.21
1664 2123 1.942712 CGTCCGGTAGCGTACATGC 60.943 63.158 13.99 0.00 0.00 4.06
1665 2124 1.140161 GTCCGGTAGCGTACATGCA 59.860 57.895 13.99 0.00 37.31 3.96
1724 2184 7.137490 TCAAGCACTGCATATATGAATTAGC 57.863 36.000 17.10 12.01 0.00 3.09
1803 2269 2.792599 GTGACGAGCTCGATCGGT 59.207 61.111 40.58 19.74 46.91 4.69
1805 2271 1.743995 TGACGAGCTCGATCGGTCA 60.744 57.895 40.58 28.88 46.91 4.02
1806 2272 1.010574 GACGAGCTCGATCGGTCAG 60.011 63.158 40.58 10.53 46.91 3.51
1807 2273 2.352915 CGAGCTCGATCGGTCAGC 60.353 66.667 32.06 16.76 43.02 4.26
1808 2274 2.026879 GAGCTCGATCGGTCAGCC 59.973 66.667 20.02 10.51 32.44 4.85
1839 2305 1.025113 TCGAATCCGACGAGCTGAGT 61.025 55.000 0.00 0.00 40.30 3.41
1938 2404 1.548269 CCCTGGAGAGATAAGATCCGC 59.452 57.143 0.00 0.00 35.78 5.54
1955 2423 1.270839 CCGCCCACGATCCAAGATAAT 60.271 52.381 0.00 0.00 43.93 1.28
2013 2481 1.802069 AGAAAACAAGAGGCGAGCTC 58.198 50.000 2.73 2.73 0.00 4.09
2101 2569 3.986116 AACGGCTCCCTCCTCCTCC 62.986 68.421 0.00 0.00 0.00 4.30
2103 2571 4.890306 GGCTCCCTCCTCCTCCCC 62.890 77.778 0.00 0.00 0.00 4.81
2124 2592 3.329889 TGCTCCTCCGGCCACAAT 61.330 61.111 2.24 0.00 0.00 2.71
2185 2653 2.260434 GCCGTCGTTCCTGCAGTA 59.740 61.111 13.81 0.00 0.00 2.74
2188 2656 2.152699 CGTCGTTCCTGCAGTAGCG 61.153 63.158 13.81 11.41 46.23 4.26
2236 2704 1.000019 CTACTCCCAGTCCCGGACA 60.000 63.158 19.95 0.00 34.60 4.02
2260 2728 2.342279 CTCGGCCTCGACACCAAA 59.658 61.111 0.00 0.00 40.88 3.28
2284 2756 5.899631 GGTAAGGTACCTTCCATGGATTA 57.100 43.478 30.38 7.16 45.52 1.75
2285 2757 5.866207 GGTAAGGTACCTTCCATGGATTAG 58.134 45.833 30.38 11.05 45.52 1.73
2290 2764 5.104485 AGGTACCTTCCATGGATTAGTTGAC 60.104 44.000 17.06 9.06 0.00 3.18
2310 2784 2.166664 ACCGTCCACTCTTCTTGCTATC 59.833 50.000 0.00 0.00 0.00 2.08
2339 2813 1.131693 TCACCACACGCGTATGAGTAG 59.868 52.381 21.01 4.33 0.00 2.57
2340 2814 1.131693 CACCACACGCGTATGAGTAGA 59.868 52.381 21.01 0.00 0.00 2.59
2356 2830 6.749923 TGAGTAGAGTATGATCGATGGATG 57.250 41.667 0.54 0.00 31.51 3.51
2503 2977 0.320247 CTGCCGCTCAGGTATCCATC 60.320 60.000 0.00 0.00 43.70 3.51
2529 3038 1.134551 TGCGTGGCTGAATGTAGCATA 60.135 47.619 0.00 0.00 45.46 3.14
2540 3049 6.259608 GCTGAATGTAGCATATGTCTTTCACT 59.740 38.462 4.29 0.00 43.17 3.41
2575 3084 8.445493 CCAAGCTAATTCAAAATTTCAATCCAC 58.555 33.333 0.00 0.00 0.00 4.02
2636 3145 3.251729 GCAGAAGAATGTCAGCTTCAACA 59.748 43.478 16.27 0.00 42.21 3.33
2768 3287 3.560481 AGCTCAAGAATGAAGATGCGATG 59.440 43.478 0.00 0.00 34.49 3.84
2769 3288 3.303857 GCTCAAGAATGAAGATGCGATGG 60.304 47.826 0.00 0.00 34.49 3.51
2770 3289 4.124970 CTCAAGAATGAAGATGCGATGGA 58.875 43.478 0.00 0.00 34.49 3.41
2772 3291 3.834489 AGAATGAAGATGCGATGGAGT 57.166 42.857 0.00 0.00 0.00 3.85
2773 3292 4.148128 AGAATGAAGATGCGATGGAGTT 57.852 40.909 0.00 0.00 0.00 3.01
2774 3293 4.125703 AGAATGAAGATGCGATGGAGTTC 58.874 43.478 0.00 0.00 0.00 3.01
2775 3294 3.548745 ATGAAGATGCGATGGAGTTCA 57.451 42.857 0.00 0.00 0.00 3.18
2776 3295 3.548745 TGAAGATGCGATGGAGTTCAT 57.451 42.857 0.00 0.00 39.13 2.57
2777 3296 4.670896 TGAAGATGCGATGGAGTTCATA 57.329 40.909 0.00 0.00 35.97 2.15
2778 3297 5.219343 TGAAGATGCGATGGAGTTCATAT 57.781 39.130 0.00 0.00 35.97 1.78
2779 3298 4.992951 TGAAGATGCGATGGAGTTCATATG 59.007 41.667 0.00 0.00 35.97 1.78
2780 3299 4.613925 AGATGCGATGGAGTTCATATGT 57.386 40.909 1.90 0.00 35.97 2.29
2781 3300 4.313282 AGATGCGATGGAGTTCATATGTG 58.687 43.478 1.90 0.00 35.97 3.21
2782 3301 3.541996 TGCGATGGAGTTCATATGTGT 57.458 42.857 1.90 0.00 35.97 3.72
2783 3302 3.197265 TGCGATGGAGTTCATATGTGTG 58.803 45.455 1.90 0.00 35.97 3.82
2784 3303 3.198068 GCGATGGAGTTCATATGTGTGT 58.802 45.455 1.90 0.00 35.97 3.72
2785 3304 3.001634 GCGATGGAGTTCATATGTGTGTG 59.998 47.826 1.90 0.00 35.97 3.82
2786 3305 4.183865 CGATGGAGTTCATATGTGTGTGT 58.816 43.478 1.90 0.00 35.97 3.72
2787 3306 5.348164 CGATGGAGTTCATATGTGTGTGTA 58.652 41.667 1.90 0.00 35.97 2.90
2788 3307 5.985530 CGATGGAGTTCATATGTGTGTGTAT 59.014 40.000 1.90 0.00 35.97 2.29
2789 3308 6.074142 CGATGGAGTTCATATGTGTGTGTATG 60.074 42.308 1.90 0.00 35.97 2.39
2790 3309 4.875536 TGGAGTTCATATGTGTGTGTATGC 59.124 41.667 1.90 0.00 0.00 3.14
2791 3310 4.273480 GGAGTTCATATGTGTGTGTATGCC 59.727 45.833 1.90 0.00 0.00 4.40
2792 3311 5.102953 AGTTCATATGTGTGTGTATGCCT 57.897 39.130 1.90 0.00 0.00 4.75
2793 3312 5.500234 AGTTCATATGTGTGTGTATGCCTT 58.500 37.500 1.90 0.00 0.00 4.35
2794 3313 5.945784 AGTTCATATGTGTGTGTATGCCTTT 59.054 36.000 1.90 0.00 0.00 3.11
2796 3315 6.435430 TCATATGTGTGTGTATGCCTTTTC 57.565 37.500 1.90 0.00 0.00 2.29
2798 3317 6.658816 TCATATGTGTGTGTATGCCTTTTCTT 59.341 34.615 1.90 0.00 0.00 2.52
2799 3318 5.789643 ATGTGTGTGTATGCCTTTTCTTT 57.210 34.783 0.00 0.00 0.00 2.52
2802 3321 5.809562 TGTGTGTGTATGCCTTTTCTTTTTG 59.190 36.000 0.00 0.00 0.00 2.44
2803 3322 4.808364 TGTGTGTATGCCTTTTCTTTTTGC 59.192 37.500 0.00 0.00 0.00 3.68
2804 3323 4.047822 TGTGTATGCCTTTTCTTTTTGCG 58.952 39.130 0.00 0.00 0.00 4.85
2805 3324 3.428534 GTGTATGCCTTTTCTTTTTGCGG 59.571 43.478 0.00 0.00 0.00 5.69
2806 3325 2.168326 ATGCCTTTTCTTTTTGCGGG 57.832 45.000 0.00 0.00 0.00 6.13
2807 3326 0.105778 TGCCTTTTCTTTTTGCGGGG 59.894 50.000 0.00 0.00 0.00 5.73
2809 3328 1.474320 GCCTTTTCTTTTTGCGGGGTT 60.474 47.619 0.00 0.00 0.00 4.11
2813 3332 4.262249 CCTTTTCTTTTTGCGGGGTTCATA 60.262 41.667 0.00 0.00 0.00 2.15
2833 3352 0.888736 TGTGTGTGTATGCAGGCCAC 60.889 55.000 5.01 0.00 0.00 5.01
2887 3406 0.613777 GGGACGTGATGGAGTTCCTT 59.386 55.000 0.00 0.00 33.23 3.36
3083 3602 9.706691 ACGTTGCTACATAATTAAGCTATGTAT 57.293 29.630 15.46 3.61 40.01 2.29
3084 3603 9.958285 CGTTGCTACATAATTAAGCTATGTATG 57.042 33.333 15.46 6.07 40.01 2.39
3131 3650 0.447406 TCAAGATCAAACGGCATGCG 59.553 50.000 12.44 9.76 0.00 4.73
3146 3665 0.736636 ATGCGTGCATGAGATTGGTG 59.263 50.000 10.93 0.00 35.03 4.17
3147 3666 1.226491 GCGTGCATGAGATTGGTGC 60.226 57.895 10.93 0.00 39.26 5.01
3289 3808 7.336427 TCCAATTTTTCATTTGACATAATGCCC 59.664 33.333 0.00 0.00 35.86 5.36
3379 3900 6.883217 AGAGCATGAGAAGTAACAATCACATT 59.117 34.615 0.00 0.00 0.00 2.71
3437 3958 1.576577 AGTGATCCTGAGATGCACCA 58.423 50.000 0.00 0.00 34.08 4.17
3472 3993 1.141881 CTCACCGGGGAGAACATCG 59.858 63.158 30.83 0.00 37.05 3.84
3506 4027 7.216317 GGTTTTTCAAAGACGTGAATATGATCG 59.784 37.037 0.00 0.00 37.36 3.69
3535 4512 1.806542 CACGTCACAAGGAAGGAATGG 59.193 52.381 0.00 0.00 0.00 3.16
3589 4566 1.254975 TAGCAGCGCCAACCTACAGA 61.255 55.000 2.29 0.00 0.00 3.41
3705 4682 1.541670 GGACGGCTTTCACCTAACACA 60.542 52.381 0.00 0.00 0.00 3.72
3719 4696 3.679980 CCTAACACAAGTCCTCATTGACG 59.320 47.826 0.00 0.00 40.26 4.35
3794 4772 1.379044 CCGGCAAGAATCAAGCCCT 60.379 57.895 9.78 0.00 45.56 5.19
3796 4774 1.017387 CGGCAAGAATCAAGCCCTAC 58.983 55.000 9.78 0.00 45.56 3.18
3799 4777 2.659428 GCAAGAATCAAGCCCTACCAT 58.341 47.619 0.00 0.00 0.00 3.55
3973 4951 3.264866 GAACTGCCTCCGACGACGT 62.265 63.158 0.00 0.00 37.88 4.34
4019 4997 4.099727 GCTAGACGGGAAGAACCTTATTCT 59.900 45.833 0.00 0.00 38.98 2.40
4031 5009 7.996758 AGAACCTTATTCTATCTTCAGGGAA 57.003 36.000 0.00 0.00 0.00 3.97
4054 5032 2.047274 ACCGCGTCACCTTCATGG 60.047 61.111 4.92 0.00 42.93 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.261825 CCTGGTGGCGTCTTTTTATTTTGA 60.262 41.667 0.00 0.00 0.00 2.69
22 23 4.394712 GCACTCGGGTCCTGGTGG 62.395 72.222 16.58 3.94 0.00 4.61
75 76 1.199624 GGTTGTGCTTTCACGCAAAG 58.800 50.000 3.56 3.56 46.01 2.77
78 79 2.109739 ACGGTTGTGCTTTCACGCA 61.110 52.632 0.00 0.00 46.01 5.24
80 81 4.588084 CACGGTTGTGCTTTCACG 57.412 55.556 0.00 0.00 46.01 4.35
110 111 2.125552 TGCTCCCGTGATGCTTCG 60.126 61.111 0.00 0.00 0.00 3.79
120 133 2.192861 TGCCAACTTTGTGCTCCCG 61.193 57.895 0.00 0.00 0.00 5.14
137 150 1.518102 GCATGTGTTTCGCAAAGTGTG 59.482 47.619 0.00 0.00 0.00 3.82
192 205 7.152645 CAGTGTACTAAGTTGTGTTCCTACAT 58.847 38.462 0.00 0.00 36.50 2.29
214 227 3.550820 TGTGCTACCATGAAAACACAGT 58.449 40.909 0.00 0.00 33.41 3.55
285 300 6.992715 ACTCATGCTTCAAAACTGTACTAACT 59.007 34.615 0.00 0.00 0.00 2.24
398 413 6.091713 CCACGTGGAAGTTATAGGTTTTACAG 59.908 42.308 31.31 0.00 37.39 2.74
441 457 6.126409 AGAATCTCGAGAAGTTGAGGTAGAT 58.874 40.000 20.91 0.00 35.12 1.98
442 458 5.502079 AGAATCTCGAGAAGTTGAGGTAGA 58.498 41.667 20.91 0.00 35.12 2.59
536 581 8.540492 CCGTATGTACTAGTCATTTGAAATGTC 58.460 37.037 16.62 11.74 0.00 3.06
537 582 8.255206 TCCGTATGTACTAGTCATTTGAAATGT 58.745 33.333 16.62 2.38 0.00 2.71
538 583 8.642908 TCCGTATGTACTAGTCATTTGAAATG 57.357 34.615 11.54 11.54 0.00 2.32
539 584 9.261180 CATCCGTATGTACTAGTCATTTGAAAT 57.739 33.333 0.00 0.00 0.00 2.17
540 585 8.255206 ACATCCGTATGTACTAGTCATTTGAAA 58.745 33.333 0.00 0.00 44.66 2.69
541 586 7.778083 ACATCCGTATGTACTAGTCATTTGAA 58.222 34.615 0.00 0.00 44.66 2.69
542 587 7.342769 ACATCCGTATGTACTAGTCATTTGA 57.657 36.000 0.00 2.08 44.66 2.69
585 630 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
586 631 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
587 632 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
593 638 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
596 641 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
603 648 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
604 649 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
605 650 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
606 651 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
607 652 6.534059 CATTTCAACAAGTGACTACATACGG 58.466 40.000 0.00 0.00 35.39 4.02
608 653 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
609 654 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
610 655 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
611 656 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
612 657 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
613 658 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
614 659 6.109156 TCTAGGCATTTCAACAAGTGACTA 57.891 37.500 0.00 0.00 38.51 2.59
615 660 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
616 661 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
617 662 6.017109 GTCTTTCTAGGCATTTCAACAAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
618 663 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
619 664 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
620 665 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
621 666 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
622 667 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
623 668 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
624 669 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
625 670 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
627 672 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
628 673 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
629 674 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
630 675 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
631 676 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
632 677 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
633 678 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
634 679 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
635 680 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
636 681 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
637 682 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
638 683 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
639 684 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
643 688 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
648 693 5.129320 GGTAAATACTCCCTCCGTTCCTAAA 59.871 44.000 0.00 0.00 0.00 1.85
651 696 3.036819 GGTAAATACTCCCTCCGTTCCT 58.963 50.000 0.00 0.00 0.00 3.36
652 697 3.036819 AGGTAAATACTCCCTCCGTTCC 58.963 50.000 0.00 0.00 0.00 3.62
657 702 5.821470 GCAAAAGTAGGTAAATACTCCCTCC 59.179 44.000 0.00 0.00 34.90 4.30
662 707 6.315642 GGAGTGGCAAAAGTAGGTAAATACTC 59.684 42.308 0.00 0.00 34.90 2.59
710 755 3.073798 TGGGTTTGCTCATGGTCTTCTAA 59.926 43.478 0.00 0.00 0.00 2.10
748 793 3.746045 AGTGGTTTCTCTGCTCGTTTA 57.254 42.857 0.00 0.00 0.00 2.01
755 800 1.404315 CGGGAGTAGTGGTTTCTCTGC 60.404 57.143 0.00 0.00 0.00 4.26
761 806 1.196766 GGGGTCGGGAGTAGTGGTTT 61.197 60.000 0.00 0.00 0.00 3.27
839 884 3.551407 GGATGGAGGCGGAGGGTC 61.551 72.222 0.00 0.00 0.00 4.46
937 982 2.112297 GGTTGGACAGTTGGGCGA 59.888 61.111 0.00 0.00 0.00 5.54
984 1029 2.941720 CCTCATGTTTTAGCTCTGCTCC 59.058 50.000 0.00 0.00 40.44 4.70
1012 1057 0.912006 AAGGAGGGAGGAAGGAGTGC 60.912 60.000 0.00 0.00 0.00 4.40
1020 1065 2.781174 GAGAGTAGAGAAGGAGGGAGGA 59.219 54.545 0.00 0.00 0.00 3.71
1040 1085 0.402861 AAGAACAAGGAGGGGTGGGA 60.403 55.000 0.00 0.00 0.00 4.37
1095 1140 8.423349 TCATCTCAAAACAACTCCATGATTTTT 58.577 29.630 0.00 0.00 0.00 1.94
1169 1215 0.038166 GGAGGAGTTTGCCATCCACA 59.962 55.000 0.00 0.00 38.12 4.17
1204 1250 0.252197 TCCATCGACTGAGACCTCGA 59.748 55.000 0.00 0.00 42.79 4.04
1243 1290 1.000843 CCGACATGACAGACAGTGGAA 59.999 52.381 0.00 0.00 0.00 3.53
1251 1298 0.532573 GCCTTCTCCGACATGACAGA 59.467 55.000 0.00 0.00 0.00 3.41
1290 1337 1.741770 GCTTCGATCCAACCGCAGT 60.742 57.895 0.00 0.00 0.00 4.40
1292 1339 2.773397 TTCGCTTCGATCCAACCGCA 62.773 55.000 0.00 0.00 35.23 5.69
1294 1341 1.999051 CTTCGCTTCGATCCAACCG 59.001 57.895 0.00 0.00 35.23 4.44
1295 1342 1.716172 GCTTCGCTTCGATCCAACC 59.284 57.895 0.00 0.00 35.23 3.77
1296 1343 1.345176 CGCTTCGCTTCGATCCAAC 59.655 57.895 0.00 0.00 35.23 3.77
1297 1344 1.809619 CCGCTTCGCTTCGATCCAA 60.810 57.895 0.00 0.00 35.23 3.53
1298 1345 2.202743 CCGCTTCGCTTCGATCCA 60.203 61.111 0.00 0.00 35.23 3.41
1299 1346 1.946650 CTCCGCTTCGCTTCGATCC 60.947 63.158 0.00 0.00 35.23 3.36
1300 1347 1.226717 ACTCCGCTTCGCTTCGATC 60.227 57.895 0.00 0.00 35.23 3.69
1301 1348 1.517257 CACTCCGCTTCGCTTCGAT 60.517 57.895 0.00 0.00 35.23 3.59
1302 1349 2.126463 CACTCCGCTTCGCTTCGA 60.126 61.111 0.00 0.00 0.00 3.71
1303 1350 3.181967 CCACTCCGCTTCGCTTCG 61.182 66.667 0.00 0.00 0.00 3.79
1304 1351 2.095252 GTCCACTCCGCTTCGCTTC 61.095 63.158 0.00 0.00 0.00 3.86
1305 1352 2.048127 GTCCACTCCGCTTCGCTT 60.048 61.111 0.00 0.00 0.00 4.68
1306 1353 4.070552 GGTCCACTCCGCTTCGCT 62.071 66.667 0.00 0.00 0.00 4.93
1314 1361 1.070289 ACTTCACTTTCGGTCCACTCC 59.930 52.381 0.00 0.00 0.00 3.85
1315 1362 2.135933 CACTTCACTTTCGGTCCACTC 58.864 52.381 0.00 0.00 0.00 3.51
1316 1363 1.202651 CCACTTCACTTTCGGTCCACT 60.203 52.381 0.00 0.00 0.00 4.00
1317 1364 1.202604 TCCACTTCACTTTCGGTCCAC 60.203 52.381 0.00 0.00 0.00 4.02
1318 1365 1.124780 TCCACTTCACTTTCGGTCCA 58.875 50.000 0.00 0.00 0.00 4.02
1319 1366 1.070289 AGTCCACTTCACTTTCGGTCC 59.930 52.381 0.00 0.00 0.00 4.46
1320 1367 2.528041 AGTCCACTTCACTTTCGGTC 57.472 50.000 0.00 0.00 0.00 4.79
1321 1368 2.288886 GCTAGTCCACTTCACTTTCGGT 60.289 50.000 0.00 0.00 0.00 4.69
1322 1369 2.288825 TGCTAGTCCACTTCACTTTCGG 60.289 50.000 0.00 0.00 0.00 4.30
1323 1370 3.026630 TGCTAGTCCACTTCACTTTCG 57.973 47.619 0.00 0.00 0.00 3.46
1357 1404 0.248825 CTCTCTCTCCATTCGCACGG 60.249 60.000 0.00 0.00 0.00 4.94
1369 1416 5.655974 TCAAACTCAGCACATATCTCTCTCT 59.344 40.000 0.00 0.00 0.00 3.10
1382 1841 0.694771 AGCATCCCTCAAACTCAGCA 59.305 50.000 0.00 0.00 0.00 4.41
1402 1861 4.523173 TCATTATACATGTCCGGACTCTCC 59.477 45.833 33.39 9.21 0.00 3.71
1439 1898 4.374828 GTCACGAAAACGCAACTCAATTAC 59.625 41.667 0.00 0.00 0.00 1.89
1466 1925 1.321474 CTTCAAACTGCCCTTGCTCA 58.679 50.000 0.00 0.00 38.71 4.26
1470 1929 1.547372 CCATCCTTCAAACTGCCCTTG 59.453 52.381 0.00 0.00 0.00 3.61
1599 2058 0.391661 CTGGGACATCTGGTTCGTGG 60.392 60.000 0.00 0.00 38.20 4.94
1663 2122 2.789845 TTTGGCCAGCACATGCATGC 62.790 55.000 26.53 15.62 46.50 4.06
1664 2123 1.017177 GTTTGGCCAGCACATGCATG 61.017 55.000 25.09 25.09 45.16 4.06
1665 2124 1.189524 AGTTTGGCCAGCACATGCAT 61.190 50.000 17.17 0.00 45.16 3.96
1723 2183 2.156098 AGCGATCTACCACTAGCTAGC 58.844 52.381 20.91 6.62 32.73 3.42
1724 2184 4.998672 ACTAAGCGATCTACCACTAGCTAG 59.001 45.833 19.44 19.44 34.24 3.42
1736 2197 1.141881 CGGCCACACTAAGCGATCT 59.858 57.895 2.24 0.00 0.00 2.75
1767 2232 0.870307 CGTGGGATTGGATCGTCGAC 60.870 60.000 5.18 5.18 0.00 4.20
1768 2233 1.317431 ACGTGGGATTGGATCGTCGA 61.317 55.000 0.00 0.00 0.00 4.20
1771 2237 0.108329 GTCACGTGGGATTGGATCGT 60.108 55.000 17.00 0.00 35.12 3.73
1781 2247 2.921538 GATCGAGCTCGTCACGTGGG 62.922 65.000 33.33 8.48 40.80 4.61
1822 2288 1.135373 TCAACTCAGCTCGTCGGATTC 60.135 52.381 0.00 0.00 0.00 2.52
1854 2320 7.523052 GCGATCTAGTCTCACTAAATGGATCTT 60.523 40.741 0.00 0.00 31.67 2.40
1862 2328 6.584488 ACTCTAGCGATCTAGTCTCACTAAA 58.416 40.000 0.00 0.00 42.28 1.85
1866 2332 9.241317 GTATATACTCTAGCGATCTAGTCTCAC 57.759 40.741 5.58 0.00 42.28 3.51
1867 2333 8.968969 TGTATATACTCTAGCGATCTAGTCTCA 58.031 37.037 13.89 0.00 42.28 3.27
1868 2334 9.241317 GTGTATATACTCTAGCGATCTAGTCTC 57.759 40.741 13.89 0.00 42.28 3.36
1869 2335 8.751242 TGTGTATATACTCTAGCGATCTAGTCT 58.249 37.037 13.89 0.00 42.28 3.24
1870 2336 8.929827 TGTGTATATACTCTAGCGATCTAGTC 57.070 38.462 13.89 0.00 42.28 2.59
1873 2339 9.099454 CACATGTGTATATACTCTAGCGATCTA 57.901 37.037 18.03 0.00 0.00 1.98
1938 2404 3.003689 GCACAATTATCTTGGATCGTGGG 59.996 47.826 0.00 0.00 0.00 4.61
2013 2481 1.479730 TCATGTCAGTCCAGCTAGCTG 59.520 52.381 33.58 33.58 43.26 4.24
2167 2635 2.486636 CTACTGCAGGAACGACGGCA 62.487 60.000 19.93 0.00 34.66 5.69
2265 2733 5.491078 TCAACTAATCCATGGAAGGTACCTT 59.509 40.000 27.43 27.43 39.23 3.50
2266 2734 5.036916 TCAACTAATCCATGGAAGGTACCT 58.963 41.667 20.67 9.21 0.00 3.08
2284 2756 1.705873 AGAAGAGTGGACGGTCAACT 58.294 50.000 17.93 17.93 0.00 3.16
2285 2757 2.135933 CAAGAAGAGTGGACGGTCAAC 58.864 52.381 7.61 7.61 0.00 3.18
2290 2764 2.482142 GGATAGCAAGAAGAGTGGACGG 60.482 54.545 0.00 0.00 0.00 4.79
2310 2784 1.577328 GCGTGTGGTGACTGGAATGG 61.577 60.000 0.00 0.00 0.00 3.16
2339 2813 4.403752 TCCATCCATCCATCGATCATACTC 59.596 45.833 0.00 0.00 0.00 2.59
2340 2814 4.356436 TCCATCCATCCATCGATCATACT 58.644 43.478 0.00 0.00 0.00 2.12
2356 2830 2.149578 CGAATCTTCCTGCATCCATCC 58.850 52.381 0.00 0.00 0.00 3.51
2529 3038 5.233083 TGGAATCAGTCAGTGAAAGACAT 57.767 39.130 0.00 0.00 39.19 3.06
2540 3049 7.523293 TTTTGAATTAGCTTGGAATCAGTCA 57.477 32.000 0.00 0.00 0.00 3.41
2575 3084 2.598589 CGCAACAACTGAATGAATGGG 58.401 47.619 0.00 0.00 0.00 4.00
2636 3145 2.450476 GTGGGGAGTTTGCTGATCAAT 58.550 47.619 0.00 0.00 34.12 2.57
2768 3287 4.273480 GGCATACACACACATATGAACTCC 59.727 45.833 10.38 0.00 31.54 3.85
2769 3288 5.118990 AGGCATACACACACATATGAACTC 58.881 41.667 10.38 0.00 31.54 3.01
2770 3289 5.102953 AGGCATACACACACATATGAACT 57.897 39.130 10.38 0.00 31.54 3.01
2772 3291 6.658816 AGAAAAGGCATACACACACATATGAA 59.341 34.615 10.38 0.00 31.54 2.57
2773 3292 6.179756 AGAAAAGGCATACACACACATATGA 58.820 36.000 10.38 0.00 31.54 2.15
2774 3293 6.441093 AGAAAAGGCATACACACACATATG 57.559 37.500 0.00 0.00 32.83 1.78
2775 3294 7.466746 AAAGAAAAGGCATACACACACATAT 57.533 32.000 0.00 0.00 0.00 1.78
2776 3295 6.892658 AAAGAAAAGGCATACACACACATA 57.107 33.333 0.00 0.00 0.00 2.29
2777 3296 5.789643 AAAGAAAAGGCATACACACACAT 57.210 34.783 0.00 0.00 0.00 3.21
2778 3297 5.590530 AAAAGAAAAGGCATACACACACA 57.409 34.783 0.00 0.00 0.00 3.72
2779 3298 5.276820 GCAAAAAGAAAAGGCATACACACAC 60.277 40.000 0.00 0.00 0.00 3.82
2780 3299 4.808364 GCAAAAAGAAAAGGCATACACACA 59.192 37.500 0.00 0.00 0.00 3.72
2781 3300 4.085107 CGCAAAAAGAAAAGGCATACACAC 60.085 41.667 0.00 0.00 0.00 3.82
2782 3301 4.047822 CGCAAAAAGAAAAGGCATACACA 58.952 39.130 0.00 0.00 0.00 3.72
2783 3302 3.428534 CCGCAAAAAGAAAAGGCATACAC 59.571 43.478 0.00 0.00 0.00 2.90
2784 3303 3.553922 CCCGCAAAAAGAAAAGGCATACA 60.554 43.478 0.00 0.00 0.00 2.29
2785 3304 2.993220 CCCGCAAAAAGAAAAGGCATAC 59.007 45.455 0.00 0.00 0.00 2.39
2786 3305 2.028567 CCCCGCAAAAAGAAAAGGCATA 60.029 45.455 0.00 0.00 0.00 3.14
2787 3306 1.270785 CCCCGCAAAAAGAAAAGGCAT 60.271 47.619 0.00 0.00 0.00 4.40
2788 3307 0.105778 CCCCGCAAAAAGAAAAGGCA 59.894 50.000 0.00 0.00 0.00 4.75
2789 3308 0.105964 ACCCCGCAAAAAGAAAAGGC 59.894 50.000 0.00 0.00 0.00 4.35
2790 3309 2.159028 TGAACCCCGCAAAAAGAAAAGG 60.159 45.455 0.00 0.00 0.00 3.11
2791 3310 3.172229 TGAACCCCGCAAAAAGAAAAG 57.828 42.857 0.00 0.00 0.00 2.27
2792 3311 3.828875 ATGAACCCCGCAAAAAGAAAA 57.171 38.095 0.00 0.00 0.00 2.29
2793 3312 4.282195 ACATATGAACCCCGCAAAAAGAAA 59.718 37.500 10.38 0.00 0.00 2.52
2794 3313 3.829601 ACATATGAACCCCGCAAAAAGAA 59.170 39.130 10.38 0.00 0.00 2.52
2796 3315 3.056891 ACACATATGAACCCCGCAAAAAG 60.057 43.478 10.38 0.00 0.00 2.27
2798 3317 2.230025 CACACATATGAACCCCGCAAAA 59.770 45.455 10.38 0.00 0.00 2.44
2799 3318 1.815613 CACACATATGAACCCCGCAAA 59.184 47.619 10.38 0.00 0.00 3.68
2802 3321 0.732571 CACACACATATGAACCCCGC 59.267 55.000 10.38 0.00 0.00 6.13
2803 3322 2.107950 ACACACACATATGAACCCCG 57.892 50.000 10.38 0.00 0.00 5.73
2804 3323 3.315191 GCATACACACACATATGAACCCC 59.685 47.826 10.38 0.00 31.54 4.95
2805 3324 3.944650 TGCATACACACACATATGAACCC 59.055 43.478 10.38 0.00 31.54 4.11
2806 3325 4.035558 CCTGCATACACACACATATGAACC 59.964 45.833 10.38 0.00 31.54 3.62
2807 3326 4.496341 GCCTGCATACACACACATATGAAC 60.496 45.833 10.38 0.00 31.54 3.18
2809 3328 3.205338 GCCTGCATACACACACATATGA 58.795 45.455 10.38 0.00 31.54 2.15
2813 3332 0.038021 TGGCCTGCATACACACACAT 59.962 50.000 3.32 0.00 0.00 3.21
2833 3352 1.443407 CACCTCCGCCTGGATGTAG 59.557 63.158 0.00 0.00 45.33 2.74
2887 3406 2.342279 CCGGCGTCCTTCTTCACA 59.658 61.111 6.01 0.00 0.00 3.58
3034 3553 1.871676 TCGACGGAGGATCTTATGTCG 59.128 52.381 19.17 19.17 42.74 4.35
3083 3602 2.731721 CAGTCGGCGCGTGTTACA 60.732 61.111 8.43 0.00 0.00 2.41
3084 3603 2.732094 ACAGTCGGCGCGTGTTAC 60.732 61.111 8.43 1.11 0.00 2.50
3085 3604 2.731721 CACAGTCGGCGCGTGTTA 60.732 61.111 8.43 0.00 0.00 2.41
3086 3605 4.578898 TCACAGTCGGCGCGTGTT 62.579 61.111 18.63 2.17 32.42 3.32
3088 3607 3.971453 ATCTCACAGTCGGCGCGTG 62.971 63.158 8.43 14.93 0.00 5.34
3188 3707 6.073548 GGCTATTGGACGACAAATTATCTGAG 60.074 42.308 0.00 0.00 43.46 3.35
3327 3847 9.625747 TTATACTGCCATGATGTTTGAGAATAA 57.374 29.630 0.00 0.00 0.00 1.40
3379 3900 2.355716 GCTAGGTGGCCTACAAACATGA 60.356 50.000 3.32 0.00 34.61 3.07
3426 3947 1.473788 CGATGATGGTGGTGCATCTCA 60.474 52.381 0.00 0.00 37.00 3.27
3431 3952 2.438254 GGCGATGATGGTGGTGCA 60.438 61.111 0.00 0.00 0.00 4.57
3437 3958 1.694169 AGGAAGGGGCGATGATGGT 60.694 57.895 0.00 0.00 0.00 3.55
3472 3993 4.109766 CGTCTTTGAAAAACCCAAAGGAC 58.890 43.478 13.51 10.09 46.25 3.85
3535 4512 1.069906 ACATCTCAAAGCGCGTGTTTC 60.070 47.619 8.43 0.00 0.00 2.78
3540 4517 1.126113 CGTAAACATCTCAAAGCGCGT 59.874 47.619 8.43 0.00 0.00 6.01
3548 4525 2.479049 GCTCTACGGCGTAAACATCTCA 60.479 50.000 21.32 0.00 0.00 3.27
3658 4635 1.966451 GTTGAGAACCAGGGTGGCG 60.966 63.158 0.00 0.00 42.67 5.69
3705 4682 0.840722 ACCCCCGTCAATGAGGACTT 60.841 55.000 4.32 0.00 35.63 3.01
3719 4696 0.984995 AAGTTGAGACTGCTACCCCC 59.015 55.000 0.00 0.00 35.91 5.40
3794 4772 9.771140 ATTATTTGGTTAAAGGTGGTAATGGTA 57.229 29.630 0.00 0.00 0.00 3.25
3799 4777 9.245481 CTGGTATTATTTGGTTAAAGGTGGTAA 57.755 33.333 0.00 0.00 0.00 2.85
3918 4896 5.204409 TGATAACCGCTACGAAATGGTAT 57.796 39.130 0.00 0.00 33.45 2.73
3923 4901 2.475111 CGCATGATAACCGCTACGAAAT 59.525 45.455 0.00 0.00 0.00 2.17
3973 4951 1.102154 CATCCTGGCGGTGCATTTTA 58.898 50.000 0.00 0.00 0.00 1.52
4037 5015 2.047274 CCATGAAGGTGACGCGGT 60.047 61.111 12.47 0.00 0.00 5.68
4042 5020 1.347707 TGTCCTGTCCATGAAGGTGAC 59.652 52.381 0.00 0.00 39.02 3.67


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

AutoCloner maintained by Alex Coulton.