Multiple sequence alignment - TraesCS5A01G434100

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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 TraesCS5A01G434100 chr5A 100.000 4944 0 0 1 4944 617211538 617206595 0.000000e+00 9130.0
1 TraesCS5A01G434100 chr5A 86.881 747 78 14 3007 3753 470929929 470930655 0.000000e+00 819.0
2 TraesCS5A01G434100 chr5D 94.660 2341 79 19 2617 4944 494217783 494215476 0.000000e+00 3589.0
3 TraesCS5A01G434100 chr5D 89.058 2632 141 64 44 2619 494220359 494217819 0.000000e+00 3129.0
4 TraesCS5A01G434100 chr5D 88.592 824 72 13 3007 3828 27284144 27284947 0.000000e+00 981.0
5 TraesCS5A01G434100 chr5D 88.988 672 55 10 3157 3828 510553684 510554336 0.000000e+00 813.0
6 TraesCS5A01G434100 chr5B 93.466 2066 93 26 2617 4669 610501629 610499593 0.000000e+00 3029.0
7 TraesCS5A01G434100 chr5B 92.213 1053 56 10 1581 2619 610502705 610501665 0.000000e+00 1467.0
8 TraesCS5A01G434100 chr5B 91.489 893 60 7 4064 4944 610306149 610305261 0.000000e+00 1214.0
9 TraesCS5A01G434100 chr5B 86.677 653 42 23 495 1119 610503810 610503175 0.000000e+00 682.0
10 TraesCS5A01G434100 chr5B 85.463 454 25 14 1 444 610504234 610503812 7.600000e-118 435.0
11 TraesCS5A01G434100 chr5B 95.896 268 10 1 3803 4069 610311504 610311237 2.730000e-117 433.0
12 TraesCS5A01G434100 chr7B 88.956 824 75 11 3007 3828 228802385 228803194 0.000000e+00 1003.0
13 TraesCS5A01G434100 chr2D 88.714 824 72 14 3007 3828 29095700 29094896 0.000000e+00 987.0
14 TraesCS5A01G434100 chr2D 85.455 110 16 0 1001 1110 495095137 495095246 1.120000e-21 115.0
15 TraesCS5A01G434100 chr4D 87.758 825 80 13 3007 3828 85851144 85850338 0.000000e+00 944.0
16 TraesCS5A01G434100 chr4D 97.297 37 1 0 41 77 62875893 62875929 4.130000e-06 63.9
17 TraesCS5A01G434100 chr3A 86.569 752 78 14 3007 3756 662598914 662598184 0.000000e+00 808.0
18 TraesCS5A01G434100 chr3A 93.182 44 3 0 41 84 739951582 739951539 1.150000e-06 65.8
19 TraesCS5A01G434100 chr2B 86.559 744 79 15 3010 3753 100102746 100102024 0.000000e+00 800.0
20 TraesCS5A01G434100 chr2B 85.455 110 16 0 1001 1110 582803074 582803183 1.120000e-21 115.0
21 TraesCS5A01G434100 chr7D 88.559 673 57 11 3157 3828 574099723 574099070 0.000000e+00 798.0
22 TraesCS5A01G434100 chr1B 90.988 344 24 5 3479 3822 289694812 289695148 1.620000e-124 457.0
23 TraesCS5A01G434100 chr3B 88.055 293 30 4 831 1119 235458654 235458363 4.740000e-90 342.0
24 TraesCS5A01G434100 chr3B 91.244 217 18 1 1740 1955 235457754 235457538 1.350000e-75 294.0
25 TraesCS5A01G434100 chr3B 95.918 147 6 0 1581 1727 235457937 235457791 6.400000e-59 239.0
26 TraesCS5A01G434100 chr3B 96.503 143 5 0 2061 2203 235444707 235444565 2.300000e-58 237.0
27 TraesCS5A01G434100 chr4A 77.218 496 79 17 4333 4818 508274032 508274503 4.910000e-65 259.0
28 TraesCS5A01G434100 chr4A 75.556 495 88 16 4333 4818 508357801 508358271 3.880000e-51 213.0
29 TraesCS5A01G434100 chr4A 75.252 497 87 18 4333 4818 508494132 508494603 2.330000e-48 204.0
30 TraesCS5A01G434100 chr4A 95.000 40 2 0 41 80 164709825 164709786 4.130000e-06 63.9
31 TraesCS5A01G434100 chr2A 84.545 110 17 0 1001 1110 638688747 638688638 5.230000e-20 110.0
32 TraesCS5A01G434100 chr6A 82.927 82 8 4 3 83 33017865 33017941 8.880000e-08 69.4
33 TraesCS5A01G434100 chr6A 82.667 75 9 2 3 77 57571697 57571767 4.130000e-06 63.9
34 TraesCS5A01G434100 chr4B 97.297 37 1 0 41 77 387389197 387389233 4.130000e-06 63.9
35 TraesCS5A01G434100 chr3D 95.000 40 2 0 41 80 573764935 573764896 4.130000e-06 63.9
36 TraesCS5A01G434100 chr6B 82.432 74 9 2 4 77 603139368 603139437 1.490000e-05 62.1
37 TraesCS5A01G434100 chr1D 82.051 78 8 5 3 76 416524892 416524817 1.490000e-05 62.1


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 TraesCS5A01G434100 chr5A 617206595 617211538 4943 True 9130.000000 9130 100.00000 1 4944 1 chr5A.!!$R1 4943
1 TraesCS5A01G434100 chr5A 470929929 470930655 726 False 819.000000 819 86.88100 3007 3753 1 chr5A.!!$F1 746
2 TraesCS5A01G434100 chr5D 494215476 494220359 4883 True 3359.000000 3589 91.85900 44 4944 2 chr5D.!!$R1 4900
3 TraesCS5A01G434100 chr5D 27284144 27284947 803 False 981.000000 981 88.59200 3007 3828 1 chr5D.!!$F1 821
4 TraesCS5A01G434100 chr5D 510553684 510554336 652 False 813.000000 813 88.98800 3157 3828 1 chr5D.!!$F2 671
5 TraesCS5A01G434100 chr5B 610499593 610504234 4641 True 1403.250000 3029 89.45475 1 4669 4 chr5B.!!$R3 4668
6 TraesCS5A01G434100 chr5B 610305261 610306149 888 True 1214.000000 1214 91.48900 4064 4944 1 chr5B.!!$R1 880
7 TraesCS5A01G434100 chr7B 228802385 228803194 809 False 1003.000000 1003 88.95600 3007 3828 1 chr7B.!!$F1 821
8 TraesCS5A01G434100 chr2D 29094896 29095700 804 True 987.000000 987 88.71400 3007 3828 1 chr2D.!!$R1 821
9 TraesCS5A01G434100 chr4D 85850338 85851144 806 True 944.000000 944 87.75800 3007 3828 1 chr4D.!!$R1 821
10 TraesCS5A01G434100 chr3A 662598184 662598914 730 True 808.000000 808 86.56900 3007 3756 1 chr3A.!!$R1 749
11 TraesCS5A01G434100 chr2B 100102024 100102746 722 True 800.000000 800 86.55900 3010 3753 1 chr2B.!!$R1 743
12 TraesCS5A01G434100 chr7D 574099070 574099723 653 True 798.000000 798 88.55900 3157 3828 1 chr7D.!!$R1 671
13 TraesCS5A01G434100 chr3B 235457538 235458654 1116 True 291.666667 342 91.73900 831 1955 3 chr3B.!!$R2 1124

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
451 469 0.032416 AGTAAGCTCCTAGCCCGGAA 60.032 55.0 0.73 0.00 43.77 4.30 F
454 472 0.032416 AAGCTCCTAGCCCGGAACTA 60.032 55.0 0.73 3.13 43.77 2.24 F
836 886 0.171903 TAACACTTCGCGGCTACTCC 59.828 55.0 6.13 0.00 0.00 3.85 F
1521 1654 0.881159 TTAAACCGTGTGCAGGACCG 60.881 55.0 0.00 0.00 0.00 4.79 F
1621 1755 0.953727 TGCAGGTTGAGTGCACAATC 59.046 50.0 21.04 9.50 45.96 2.67 F
3355 3574 0.832135 TCCTCGTCCCAGCTCACTTT 60.832 55.0 0.00 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1966 0.179215 CATTTCAAGTCGGCGACAGC 60.179 55.0 37.71 15.24 44.18 4.40 R
2222 2392 0.242286 CCGATATGCTCAGGTCTCCG 59.758 60.0 0.00 0.00 0.00 4.63 R
2249 2419 0.393820 TGAAAACTCGGGTAAGCCGT 59.606 50.0 0.00 0.00 34.97 5.68 R
3077 3292 0.748005 CCCAGGAGCCAACATTACCG 60.748 60.0 0.00 0.00 0.00 4.02 R
3517 3749 0.961753 TCGCAGCCTCGATGATGTAT 59.038 50.0 7.76 0.00 33.02 2.29 R
4245 4489 0.313987 ACTCACGCAGTTCATGACGA 59.686 50.0 10.08 0.00 41.61 4.20 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
76 77 5.932883 GCCTTATATTTAGAAACGGAGGGAG 59.067 44.000 0.00 0.00 0.00 4.30
77 78 5.932883 CCTTATATTTAGAAACGGAGGGAGC 59.067 44.000 0.00 0.00 0.00 4.70
78 79 6.463897 CCTTATATTTAGAAACGGAGGGAGCA 60.464 42.308 0.00 0.00 0.00 4.26
79 80 2.762535 TTTAGAAACGGAGGGAGCAG 57.237 50.000 0.00 0.00 0.00 4.24
125 127 1.693606 TGTGAGCATGAAGTGTCAGGA 59.306 47.619 0.00 0.00 37.78 3.86
131 133 2.094894 GCATGAAGTGTCAGGAATCACG 59.905 50.000 0.00 0.00 37.78 4.35
175 177 0.735978 CACCGTCAGCGTATCAGCAA 60.736 55.000 0.00 0.00 40.15 3.91
176 178 0.037697 ACCGTCAGCGTATCAGCAAA 60.038 50.000 0.00 0.00 40.15 3.68
208 211 3.799753 CTGTGCAGCCGGTACATC 58.200 61.111 1.90 0.00 41.45 3.06
220 228 1.749063 CGGTACATCCACAGCTCAGTA 59.251 52.381 0.00 0.00 35.57 2.74
228 236 5.104776 ACATCCACAGCTCAGTACATACATT 60.105 40.000 0.00 0.00 0.00 2.71
229 237 4.758688 TCCACAGCTCAGTACATACATTG 58.241 43.478 0.00 0.00 0.00 2.82
238 246 8.023706 AGCTCAGTACATACATTGATACATACG 58.976 37.037 0.00 0.00 0.00 3.06
239 247 7.808381 GCTCAGTACATACATTGATACATACGT 59.192 37.037 0.00 0.00 0.00 3.57
242 250 9.887406 CAGTACATACATTGATACATACGTACA 57.113 33.333 0.00 0.00 0.00 2.90
246 254 9.569167 ACATACATTGATACATACGTACATAGC 57.431 33.333 0.00 0.00 0.00 2.97
247 255 9.567848 CATACATTGATACATACGTACATAGCA 57.432 33.333 0.00 0.00 0.00 3.49
248 256 7.869016 ACATTGATACATACGTACATAGCAC 57.131 36.000 0.00 0.00 0.00 4.40
249 257 7.430441 ACATTGATACATACGTACATAGCACA 58.570 34.615 0.00 0.00 0.00 4.57
250 258 7.381408 ACATTGATACATACGTACATAGCACAC 59.619 37.037 0.00 0.00 0.00 3.82
251 259 5.765176 TGATACATACGTACATAGCACACC 58.235 41.667 0.00 0.00 0.00 4.16
252 260 5.533528 TGATACATACGTACATAGCACACCT 59.466 40.000 0.00 0.00 0.00 4.00
265 273 1.130561 GCACACCTAACCGATTTGAGC 59.869 52.381 0.00 0.00 0.00 4.26
309 323 2.050144 AGAGGCTTCCTTGAACACTCA 58.950 47.619 0.00 0.00 31.76 3.41
379 393 2.433838 CAGCTGTCGGCAGTCTGG 60.434 66.667 24.62 12.21 44.32 3.86
415 429 1.951209 TGGCCCTAGAACAGTGATCA 58.049 50.000 0.00 0.00 0.00 2.92
444 462 8.905660 TGTAGTAGATGTTAGTAAGCTCCTAG 57.094 38.462 0.00 0.00 0.00 3.02
445 463 6.887626 AGTAGATGTTAGTAAGCTCCTAGC 57.112 41.667 0.00 0.00 42.84 3.42
446 464 5.771165 AGTAGATGTTAGTAAGCTCCTAGCC 59.229 44.000 0.00 0.00 43.77 3.93
447 465 3.898741 AGATGTTAGTAAGCTCCTAGCCC 59.101 47.826 0.00 0.00 43.77 5.19
448 466 2.029623 TGTTAGTAAGCTCCTAGCCCG 58.970 52.381 0.00 0.00 43.77 6.13
449 467 1.340568 GTTAGTAAGCTCCTAGCCCGG 59.659 57.143 0.00 0.00 43.77 5.73
450 468 0.848735 TAGTAAGCTCCTAGCCCGGA 59.151 55.000 0.73 0.00 43.77 5.14
451 469 0.032416 AGTAAGCTCCTAGCCCGGAA 60.032 55.000 0.73 0.00 43.77 4.30
452 470 0.104487 GTAAGCTCCTAGCCCGGAAC 59.896 60.000 0.73 0.00 43.77 3.62
453 471 0.032416 TAAGCTCCTAGCCCGGAACT 60.032 55.000 0.73 1.77 43.77 3.01
454 472 0.032416 AAGCTCCTAGCCCGGAACTA 60.032 55.000 0.73 3.13 43.77 2.24
455 473 0.756070 AGCTCCTAGCCCGGAACTAC 60.756 60.000 0.73 0.00 43.77 2.73
456 474 0.756070 GCTCCTAGCCCGGAACTACT 60.756 60.000 0.73 0.00 34.48 2.57
457 475 1.033574 CTCCTAGCCCGGAACTACTG 58.966 60.000 0.73 0.00 31.44 2.74
458 476 0.627451 TCCTAGCCCGGAACTACTGA 59.373 55.000 0.73 0.00 0.00 3.41
459 477 1.033574 CCTAGCCCGGAACTACTGAG 58.966 60.000 0.73 0.00 0.00 3.35
460 478 0.386113 CTAGCCCGGAACTACTGAGC 59.614 60.000 0.73 0.00 0.00 4.26
461 479 0.323999 TAGCCCGGAACTACTGAGCA 60.324 55.000 0.73 0.00 0.00 4.26
462 480 1.153549 GCCCGGAACTACTGAGCAG 60.154 63.158 0.73 0.00 0.00 4.24
464 482 1.517257 CCGGAACTACTGAGCAGCG 60.517 63.158 0.00 0.00 0.00 5.18
465 483 2.161486 CGGAACTACTGAGCAGCGC 61.161 63.158 0.00 0.00 0.00 5.92
466 484 1.216710 GGAACTACTGAGCAGCGCT 59.783 57.895 2.64 2.64 43.88 5.92
475 493 3.535962 AGCAGCGCTCCTCCTAGC 61.536 66.667 7.13 6.17 30.62 3.42
476 494 4.600576 GCAGCGCTCCTCCTAGCC 62.601 72.222 7.13 0.00 39.43 3.93
477 495 2.837291 CAGCGCTCCTCCTAGCCT 60.837 66.667 7.13 0.00 39.43 4.58
478 496 1.529478 CAGCGCTCCTCCTAGCCTA 60.529 63.158 7.13 0.00 39.43 3.93
479 497 1.228429 AGCGCTCCTCCTAGCCTAG 60.228 63.158 2.64 0.00 39.43 3.02
480 498 2.926420 GCGCTCCTCCTAGCCTAGC 61.926 68.421 0.00 0.00 39.43 3.42
481 499 1.529478 CGCTCCTCCTAGCCTAGCA 60.529 63.158 0.00 0.00 39.43 3.49
482 500 1.801309 CGCTCCTCCTAGCCTAGCAC 61.801 65.000 0.00 0.00 39.43 4.40
483 501 1.468506 GCTCCTCCTAGCCTAGCACC 61.469 65.000 0.00 0.00 36.45 5.01
484 502 0.187361 CTCCTCCTAGCCTAGCACCT 59.813 60.000 0.00 0.00 0.00 4.00
485 503 0.186386 TCCTCCTAGCCTAGCACCTC 59.814 60.000 0.00 0.00 0.00 3.85
486 504 0.187361 CCTCCTAGCCTAGCACCTCT 59.813 60.000 0.00 0.00 0.00 3.69
509 527 7.002276 TCTTCTAAACTAAACAAAAGGGGAGG 58.998 38.462 0.00 0.00 0.00 4.30
554 572 4.763073 TGATGCTCTTCAATCTGGTACTG 58.237 43.478 0.00 0.00 0.00 2.74
566 584 2.175069 TCTGGTACTGGTAGGCTAGGAG 59.825 54.545 0.00 0.00 0.00 3.69
567 585 1.928077 TGGTACTGGTAGGCTAGGAGT 59.072 52.381 9.64 9.64 0.00 3.85
568 586 3.125656 TGGTACTGGTAGGCTAGGAGTA 58.874 50.000 0.00 1.42 0.00 2.59
569 587 3.137913 TGGTACTGGTAGGCTAGGAGTAG 59.862 52.174 11.21 2.23 0.00 2.57
570 588 3.138098 GGTACTGGTAGGCTAGGAGTAGT 59.862 52.174 11.21 6.94 0.00 2.73
571 589 4.349342 GGTACTGGTAGGCTAGGAGTAGTA 59.651 50.000 11.21 6.18 0.00 1.82
572 590 4.710313 ACTGGTAGGCTAGGAGTAGTAG 57.290 50.000 0.00 0.00 0.00 2.57
664 682 7.925483 CGAGAATCAGATCTTGTTCTTATCCTT 59.075 37.037 16.52 0.00 31.63 3.36
812 862 3.043713 TCTTTGTGCCGCTGCTCG 61.044 61.111 0.70 0.00 38.71 5.03
828 878 1.674611 CTCGCCACTAACACTTCGCG 61.675 60.000 0.00 0.00 40.88 5.87
836 886 0.171903 TAACACTTCGCGGCTACTCC 59.828 55.000 6.13 0.00 0.00 3.85
911 967 9.872757 GTTTAATCTTTTTGTCTCGTGTGATTA 57.127 29.630 0.00 0.00 0.00 1.75
913 969 7.730364 AATCTTTTTGTCTCGTGTGATTAGT 57.270 32.000 0.00 0.00 0.00 2.24
914 970 6.525121 TCTTTTTGTCTCGTGTGATTAGTG 57.475 37.500 0.00 0.00 0.00 2.74
921 977 4.386049 GTCTCGTGTGATTAGTGTTCTTGG 59.614 45.833 0.00 0.00 0.00 3.61
925 983 5.408299 TCGTGTGATTAGTGTTCTTGGATTG 59.592 40.000 0.00 0.00 0.00 2.67
926 984 5.393962 GTGTGATTAGTGTTCTTGGATTGC 58.606 41.667 0.00 0.00 0.00 3.56
930 988 5.880332 TGATTAGTGTTCTTGGATTGCTACC 59.120 40.000 0.00 0.00 0.00 3.18
931 989 5.499004 TTAGTGTTCTTGGATTGCTACCT 57.501 39.130 0.00 0.00 0.00 3.08
943 1001 4.446311 GGATTGCTACCTATGATGTTGGGT 60.446 45.833 0.00 0.00 36.02 4.51
948 1006 4.576463 GCTACCTATGATGTTGGGTTTCTG 59.424 45.833 0.00 0.00 33.74 3.02
1132 1190 5.770162 GTGATTATTCCTTGATCCCGGATTT 59.230 40.000 0.73 0.00 0.00 2.17
1134 1192 6.838612 TGATTATTCCTTGATCCCGGATTTTT 59.161 34.615 0.73 0.00 0.00 1.94
1323 1447 5.046950 AGGCTACCAGATTATCTTCGGATTC 60.047 44.000 5.71 0.00 36.01 2.52
1356 1480 8.197592 TCCAACCTACTACTTCACTTGATTTA 57.802 34.615 0.00 0.00 0.00 1.40
1392 1516 4.827284 TGGGGAACTTCACTTGATTTTCTC 59.173 41.667 0.00 0.00 0.00 2.87
1401 1525 5.917462 TCACTTGATTTTCTCTCTCACACA 58.083 37.500 0.00 0.00 0.00 3.72
1406 1530 6.166984 TGATTTTCTCTCTCACACACTCTT 57.833 37.500 0.00 0.00 0.00 2.85
1411 1535 6.716934 TTCTCTCTCACACACTCTTACTTT 57.283 37.500 0.00 0.00 0.00 2.66
1412 1536 6.320494 TCTCTCTCACACACTCTTACTTTC 57.680 41.667 0.00 0.00 0.00 2.62
1413 1537 5.241949 TCTCTCTCACACACTCTTACTTTCC 59.758 44.000 0.00 0.00 0.00 3.13
1414 1543 4.281182 TCTCTCACACACTCTTACTTTCCC 59.719 45.833 0.00 0.00 0.00 3.97
1418 1547 6.037786 TCACACACTCTTACTTTCCCTATG 57.962 41.667 0.00 0.00 0.00 2.23
1508 1641 5.410746 GCCACTTACTCTGTAAGGTTAAACC 59.589 44.000 18.05 0.00 38.99 3.27
1521 1654 0.881159 TTAAACCGTGTGCAGGACCG 60.881 55.000 0.00 0.00 0.00 4.79
1528 1661 1.145803 GTGTGCAGGACCGTTCTAAC 58.854 55.000 0.00 0.00 0.00 2.34
1541 1674 6.426025 GGACCGTTCTAACTTTTGAGTATGTT 59.574 38.462 0.00 0.00 0.00 2.71
1543 1676 7.636326 ACCGTTCTAACTTTTGAGTATGTTTG 58.364 34.615 0.00 0.00 0.00 2.93
1554 1687 8.840833 TTTTGAGTATGTTTGCTGTCTATGTA 57.159 30.769 0.00 0.00 0.00 2.29
1557 1690 6.535150 TGAGTATGTTTGCTGTCTATGTAAGC 59.465 38.462 0.00 0.00 37.46 3.09
1559 1692 7.782049 AGTATGTTTGCTGTCTATGTAAGCTA 58.218 34.615 0.00 0.00 37.82 3.32
1621 1755 0.953727 TGCAGGTTGAGTGCACAATC 59.046 50.000 21.04 9.50 45.96 2.67
1780 1938 7.341030 TCTTCTGTTCATCATGATACAACCAT 58.659 34.615 19.77 0.00 0.00 3.55
1784 1942 6.186234 TGTTCATCATGATACAACCATCCAA 58.814 36.000 19.77 4.94 0.00 3.53
1793 1951 5.822519 TGATACAACCATCCAATAAGCACTC 59.177 40.000 0.00 0.00 0.00 3.51
1806 1966 2.697425 CACTCGATTCTTGCCGCG 59.303 61.111 0.00 0.00 0.00 6.46
1833 1993 2.084546 CCGACTTGAAATGGTCCTTCC 58.915 52.381 0.00 0.00 0.00 3.46
1854 2014 3.433615 CCGCATAAATTCGATCTCCTTCC 59.566 47.826 0.00 0.00 0.00 3.46
1868 2028 1.825474 TCCTTCCGGAATCTGTCAGAC 59.175 52.381 19.21 0.00 36.03 3.51
1883 2043 6.216569 TCTGTCAGACAGTTGAATGACTTAC 58.783 40.000 26.65 0.03 46.03 2.34
1964 2124 8.161754 CAAAGCTATTTTGGAAATTAGTCACG 57.838 34.615 0.00 0.00 41.99 4.35
2001 2161 7.255625 GCTACTATACTGGATCACATTCTGACA 60.256 40.741 0.00 0.00 0.00 3.58
2002 2162 7.609097 ACTATACTGGATCACATTCTGACAT 57.391 36.000 0.00 0.00 0.00 3.06
2003 2163 8.027524 ACTATACTGGATCACATTCTGACATT 57.972 34.615 0.00 0.00 0.00 2.71
2004 2164 8.147058 ACTATACTGGATCACATTCTGACATTC 58.853 37.037 0.00 0.00 0.00 2.67
2005 2165 5.432680 ACTGGATCACATTCTGACATTCT 57.567 39.130 0.00 0.00 0.00 2.40
2006 2166 5.183969 ACTGGATCACATTCTGACATTCTG 58.816 41.667 0.00 0.00 0.00 3.02
2007 2167 5.046087 ACTGGATCACATTCTGACATTCTGA 60.046 40.000 0.00 0.00 0.00 3.27
2008 2168 5.181009 TGGATCACATTCTGACATTCTGAC 58.819 41.667 0.00 0.00 0.00 3.51
2101 2270 6.989759 TCATAGTAAGTTCTTGCACTGACAAA 59.010 34.615 0.00 0.00 31.01 2.83
2213 2383 1.809207 CGCTAAAGGTGGCATTGGG 59.191 57.895 0.00 0.00 0.00 4.12
2318 2488 1.296392 CACCGATGTTCCAGCTCCA 59.704 57.895 0.00 0.00 0.00 3.86
2384 2554 9.823098 CATATTTATTATTTCTCTGCAGAGTGC 57.177 33.333 36.32 0.00 45.29 4.40
2600 2773 3.380637 AGATCAAATGTGGAAGATGCAGC 59.619 43.478 0.00 0.00 0.00 5.25
2607 2780 3.093814 TGTGGAAGATGCAGCATTTGAT 58.906 40.909 9.90 0.00 0.00 2.57
2937 3150 1.867865 TCGCACAATACGCACTTTTGA 59.132 42.857 0.00 0.00 0.00 2.69
2964 3177 7.668469 ACTTTATGGTTACAAAAGGGAGTAAGG 59.332 37.037 8.27 0.00 35.09 2.69
2965 3178 4.376225 TGGTTACAAAAGGGAGTAAGGG 57.624 45.455 0.00 0.00 31.45 3.95
2966 3179 3.982052 TGGTTACAAAAGGGAGTAAGGGA 59.018 43.478 0.00 0.00 31.45 4.20
2967 3180 4.042435 TGGTTACAAAAGGGAGTAAGGGAG 59.958 45.833 0.00 0.00 31.45 4.30
2968 3181 2.881111 ACAAAAGGGAGTAAGGGAGC 57.119 50.000 0.00 0.00 0.00 4.70
2969 3182 2.062636 ACAAAAGGGAGTAAGGGAGCA 58.937 47.619 0.00 0.00 0.00 4.26
2970 3183 2.445525 ACAAAAGGGAGTAAGGGAGCAA 59.554 45.455 0.00 0.00 0.00 3.91
2971 3184 3.084786 CAAAAGGGAGTAAGGGAGCAAG 58.915 50.000 0.00 0.00 0.00 4.01
3054 3268 6.395426 TTGCAGAGATAAGCAATTATTGGG 57.605 37.500 7.08 0.00 44.98 4.12
3077 3292 3.244181 TGCTTTGCCTTTTTCAGGGATTC 60.244 43.478 0.00 0.00 43.97 2.52
3122 3337 1.467734 CAACTGATCACTGAAGCTGGC 59.532 52.381 0.00 0.00 0.00 4.85
3355 3574 0.832135 TCCTCGTCCCAGCTCACTTT 60.832 55.000 0.00 0.00 0.00 2.66
3358 3577 2.693591 CCTCGTCCCAGCTCACTTTATA 59.306 50.000 0.00 0.00 0.00 0.98
3359 3578 3.322254 CCTCGTCCCAGCTCACTTTATAT 59.678 47.826 0.00 0.00 0.00 0.86
3394 3613 5.614308 TCAGATTTCTGCTCTGAACTTCAA 58.386 37.500 2.60 0.00 44.59 2.69
3480 3712 5.649782 AGGCTGTTCTTAACCATGATTTG 57.350 39.130 0.00 0.00 0.00 2.32
3517 3749 2.037381 TGCTGATGCCATCAAAGCAAAA 59.963 40.909 16.55 0.00 44.83 2.44
3947 4179 3.157252 GCTGGGAGGCCTGATCGA 61.157 66.667 12.00 0.00 0.00 3.59
3948 4180 2.818132 CTGGGAGGCCTGATCGAC 59.182 66.667 12.00 0.00 0.00 4.20
4097 4330 1.446966 GAGAGACCGGCAGAACAGC 60.447 63.158 0.00 0.00 0.00 4.40
4105 4338 2.561885 GCAGAACAGCAGCAGCAG 59.438 61.111 3.17 0.00 45.49 4.24
4167 4400 6.983890 ACAGCAATGTAATTCGGTTTCTTTTT 59.016 30.769 0.00 0.00 31.22 1.94
4219 4458 5.293324 TGCGTGAGTCGATTTTATTAGCATT 59.707 36.000 0.00 0.00 42.86 3.56
4220 4459 6.183360 TGCGTGAGTCGATTTTATTAGCATTT 60.183 34.615 0.00 0.00 42.86 2.32
4223 4462 7.399523 GTGAGTCGATTTTATTAGCATTTCGT 58.600 34.615 0.00 0.00 0.00 3.85
4230 4469 7.269084 CGATTTTATTAGCATTTCGTATGGCAG 59.731 37.037 0.00 0.00 0.00 4.85
4245 4489 2.939261 GCAGCAAGCCAGCCAACAT 61.939 57.895 0.00 0.00 37.23 2.71
4261 4505 1.070821 ACATCGTCATGAACTGCGTG 58.929 50.000 0.00 1.30 33.72 5.34
4279 4523 1.226717 GAGTCGATGAGTGGGTCGC 60.227 63.158 0.00 0.00 37.74 5.19
4370 4614 4.452733 GAACCCGGCGTCCTCCAG 62.453 72.222 6.01 0.00 0.00 3.86
4443 4687 3.083997 CCCTCCAGGTCCCCGAAG 61.084 72.222 0.00 0.00 0.00 3.79
4709 4953 1.435105 GCGGTACTAGTTCGGGGTC 59.565 63.158 16.42 1.10 0.00 4.46
4820 5076 2.656651 CGCTTCTCGCTCCATCGG 60.657 66.667 0.00 0.00 36.13 4.18
4880 5137 4.104417 ACGAGAGTCACGGCGAGC 62.104 66.667 16.62 1.82 44.19 5.03
4923 5180 1.935400 ATGTGATGGGGGCAAGGGA 60.935 57.895 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 1.002087 CAAGTACTGCTCCCTCCGTTT 59.998 52.381 0.00 0.00 0.00 3.60
78 79 2.691526 TGTCCGTCAACAGTCAAGTACT 59.308 45.455 0.00 0.00 39.81 2.73
79 80 3.088194 TGTCCGTCAACAGTCAAGTAC 57.912 47.619 0.00 0.00 0.00 2.73
95 97 4.637534 ACTTCATGCTCACAATACATGTCC 59.362 41.667 0.00 0.00 41.46 4.02
131 133 1.605500 CATGCATGCACGTGTAACAC 58.394 50.000 25.37 7.16 35.74 3.32
147 149 1.759293 CGCTGACGGTGATGAGCATG 61.759 60.000 0.00 0.00 34.97 4.06
195 197 1.815421 CTGTGGATGTACCGGCTGC 60.815 63.158 0.00 0.00 42.61 5.25
198 200 1.521681 GAGCTGTGGATGTACCGGC 60.522 63.158 0.00 0.00 42.61 6.13
201 204 2.496070 TGTACTGAGCTGTGGATGTACC 59.504 50.000 0.00 0.00 39.54 3.34
208 211 4.758688 TCAATGTATGTACTGAGCTGTGG 58.241 43.478 0.00 0.00 0.00 4.17
220 228 9.569167 GCTATGTACGTATGTATCAATGTATGT 57.431 33.333 0.00 0.00 32.11 2.29
228 236 5.533528 AGGTGTGCTATGTACGTATGTATCA 59.466 40.000 0.00 0.00 32.11 2.15
229 237 6.010294 AGGTGTGCTATGTACGTATGTATC 57.990 41.667 0.00 0.00 32.11 2.24
238 246 3.788333 TCGGTTAGGTGTGCTATGTAC 57.212 47.619 0.00 0.00 0.00 2.90
239 247 5.105269 TCAAATCGGTTAGGTGTGCTATGTA 60.105 40.000 0.00 0.00 0.00 2.29
240 248 3.906720 AATCGGTTAGGTGTGCTATGT 57.093 42.857 0.00 0.00 0.00 2.29
241 249 4.188462 TCAAATCGGTTAGGTGTGCTATG 58.812 43.478 0.00 0.00 0.00 2.23
242 250 4.442706 CTCAAATCGGTTAGGTGTGCTAT 58.557 43.478 0.00 0.00 0.00 2.97
243 251 3.857052 CTCAAATCGGTTAGGTGTGCTA 58.143 45.455 0.00 0.00 0.00 3.49
244 252 2.699954 CTCAAATCGGTTAGGTGTGCT 58.300 47.619 0.00 0.00 0.00 4.40
245 253 1.130561 GCTCAAATCGGTTAGGTGTGC 59.869 52.381 0.00 0.00 0.00 4.57
246 254 2.416547 CTGCTCAAATCGGTTAGGTGTG 59.583 50.000 0.00 0.00 0.00 3.82
247 255 2.038557 ACTGCTCAAATCGGTTAGGTGT 59.961 45.455 0.00 0.00 0.00 4.16
248 256 2.699954 ACTGCTCAAATCGGTTAGGTG 58.300 47.619 0.00 0.00 0.00 4.00
249 257 4.546829 TTACTGCTCAAATCGGTTAGGT 57.453 40.909 0.00 0.00 0.00 3.08
250 258 5.235186 CAGATTACTGCTCAAATCGGTTAGG 59.765 44.000 0.00 0.00 37.22 2.69
251 259 6.042777 TCAGATTACTGCTCAAATCGGTTAG 58.957 40.000 0.00 0.00 43.17 2.34
252 260 5.972935 TCAGATTACTGCTCAAATCGGTTA 58.027 37.500 0.00 0.00 43.17 2.85
265 273 4.673580 GCATGTGGCAACTTCAGATTACTG 60.674 45.833 0.00 0.00 43.97 2.74
379 393 3.317430 GGGCCAACATCTGAATGAAGATC 59.683 47.826 4.39 0.00 34.60 2.75
415 429 9.819267 GGAGCTTACTAACATCTACTACAAAAT 57.181 33.333 0.00 0.00 0.00 1.82
444 462 1.153549 CTGCTCAGTAGTTCCGGGC 60.154 63.158 0.00 0.00 0.00 6.13
445 463 1.153549 GCTGCTCAGTAGTTCCGGG 60.154 63.158 0.00 0.00 0.00 5.73
446 464 1.517257 CGCTGCTCAGTAGTTCCGG 60.517 63.158 0.00 0.00 0.00 5.14
447 465 2.161486 GCGCTGCTCAGTAGTTCCG 61.161 63.158 0.00 0.00 0.00 4.30
448 466 1.216710 AGCGCTGCTCAGTAGTTCC 59.783 57.895 10.39 0.00 30.62 3.62
449 467 4.900154 AGCGCTGCTCAGTAGTTC 57.100 55.556 10.39 0.00 30.62 3.01
458 476 3.535962 GCTAGGAGGAGCGCTGCT 61.536 66.667 32.73 32.73 43.88 4.24
459 477 4.600576 GGCTAGGAGGAGCGCTGC 62.601 72.222 22.65 22.65 43.83 5.25
460 478 1.523154 CTAGGCTAGGAGGAGCGCTG 61.523 65.000 18.48 0.00 43.83 5.18
461 479 1.228429 CTAGGCTAGGAGGAGCGCT 60.228 63.158 11.27 11.27 43.83 5.92
462 480 2.926420 GCTAGGCTAGGAGGAGCGC 61.926 68.421 22.40 0.00 43.83 5.92
464 482 1.468506 GGTGCTAGGCTAGGAGGAGC 61.469 65.000 22.40 10.56 42.05 4.70
465 483 0.187361 AGGTGCTAGGCTAGGAGGAG 59.813 60.000 22.40 0.00 0.00 3.69
466 484 0.186386 GAGGTGCTAGGCTAGGAGGA 59.814 60.000 22.40 0.00 0.00 3.71
467 485 0.187361 AGAGGTGCTAGGCTAGGAGG 59.813 60.000 22.40 0.00 0.00 4.30
468 486 1.960689 GAAGAGGTGCTAGGCTAGGAG 59.039 57.143 22.40 0.60 0.00 3.69
469 487 1.571457 AGAAGAGGTGCTAGGCTAGGA 59.429 52.381 22.40 17.67 0.00 2.94
470 488 2.080654 AGAAGAGGTGCTAGGCTAGG 57.919 55.000 22.40 5.26 0.00 3.02
471 489 4.647399 AGTTTAGAAGAGGTGCTAGGCTAG 59.353 45.833 17.33 17.33 0.00 3.42
472 490 4.611367 AGTTTAGAAGAGGTGCTAGGCTA 58.389 43.478 0.00 0.00 0.00 3.93
473 491 3.445987 AGTTTAGAAGAGGTGCTAGGCT 58.554 45.455 0.00 0.00 0.00 4.58
474 492 3.897141 AGTTTAGAAGAGGTGCTAGGC 57.103 47.619 0.00 0.00 0.00 3.93
475 493 6.698380 TGTTTAGTTTAGAAGAGGTGCTAGG 58.302 40.000 0.00 0.00 0.00 3.02
476 494 8.603242 TTTGTTTAGTTTAGAAGAGGTGCTAG 57.397 34.615 0.00 0.00 0.00 3.42
477 495 8.967664 TTTTGTTTAGTTTAGAAGAGGTGCTA 57.032 30.769 0.00 0.00 0.00 3.49
478 496 7.013369 CCTTTTGTTTAGTTTAGAAGAGGTGCT 59.987 37.037 0.00 0.00 0.00 4.40
479 497 7.139392 CCTTTTGTTTAGTTTAGAAGAGGTGC 58.861 38.462 0.00 0.00 0.00 5.01
480 498 7.255486 CCCCTTTTGTTTAGTTTAGAAGAGGTG 60.255 40.741 0.00 0.00 0.00 4.00
481 499 6.776116 CCCCTTTTGTTTAGTTTAGAAGAGGT 59.224 38.462 0.00 0.00 0.00 3.85
482 500 7.002276 TCCCCTTTTGTTTAGTTTAGAAGAGG 58.998 38.462 0.00 0.00 0.00 3.69
483 501 7.175119 CCTCCCCTTTTGTTTAGTTTAGAAGAG 59.825 40.741 0.00 0.00 0.00 2.85
484 502 7.002276 CCTCCCCTTTTGTTTAGTTTAGAAGA 58.998 38.462 0.00 0.00 0.00 2.87
485 503 6.776116 ACCTCCCCTTTTGTTTAGTTTAGAAG 59.224 38.462 0.00 0.00 0.00 2.85
486 504 6.548251 CACCTCCCCTTTTGTTTAGTTTAGAA 59.452 38.462 0.00 0.00 0.00 2.10
509 527 2.158957 TCTATGCCAAGGAATCGACCAC 60.159 50.000 0.00 0.00 0.00 4.16
554 572 5.823861 ACTACTACTACTCCTAGCCTACC 57.176 47.826 0.00 0.00 0.00 3.18
569 587 8.962111 GCACTCAATACCGTAATTAACTACTAC 58.038 37.037 0.00 0.00 0.00 2.73
570 588 8.685427 TGCACTCAATACCGTAATTAACTACTA 58.315 33.333 0.00 0.00 0.00 1.82
571 589 7.549839 TGCACTCAATACCGTAATTAACTACT 58.450 34.615 0.00 0.00 0.00 2.57
572 590 7.703621 TCTGCACTCAATACCGTAATTAACTAC 59.296 37.037 0.00 0.00 0.00 2.73
592 610 4.767255 CCCGAGCCCTGTCTGCAC 62.767 72.222 0.00 0.00 0.00 4.57
594 612 4.459089 GACCCGAGCCCTGTCTGC 62.459 72.222 0.00 0.00 0.00 4.26
690 717 9.533253 CAAAAAGCAGAGGAGATTTTTCTTTTA 57.467 29.630 0.00 0.00 42.97 1.52
747 779 3.701205 TGCATATATAGGCACACTGGG 57.299 47.619 17.63 0.00 38.15 4.45
748 780 4.805719 CGTATGCATATATAGGCACACTGG 59.194 45.833 23.65 9.52 46.26 4.00
812 862 3.165498 CCGCGAAGTGTTAGTGGC 58.835 61.111 8.23 0.00 35.45 5.01
828 878 4.208686 CCGGCGAGTGGAGTAGCC 62.209 72.222 9.30 0.00 45.67 3.93
836 886 3.805422 TGCTTTTATATTACCGGCGAGTG 59.195 43.478 9.30 0.00 0.00 3.51
842 895 9.449719 AAGGATAATCTGCTTTTATATTACCGG 57.550 33.333 0.00 0.00 30.16 5.28
911 967 5.189736 TCATAGGTAGCAATCCAAGAACACT 59.810 40.000 0.00 0.00 0.00 3.55
913 969 5.692115 TCATAGGTAGCAATCCAAGAACA 57.308 39.130 0.00 0.00 0.00 3.18
914 970 6.058183 ACATCATAGGTAGCAATCCAAGAAC 58.942 40.000 0.00 0.00 0.00 3.01
921 977 4.718961 ACCCAACATCATAGGTAGCAATC 58.281 43.478 0.00 0.00 0.00 2.67
925 983 4.576463 CAGAAACCCAACATCATAGGTAGC 59.424 45.833 0.00 0.00 30.63 3.58
926 984 5.104527 TCCAGAAACCCAACATCATAGGTAG 60.105 44.000 0.00 0.00 30.63 3.18
930 988 4.823989 GGATCCAGAAACCCAACATCATAG 59.176 45.833 6.95 0.00 0.00 2.23
931 989 4.685848 CGGATCCAGAAACCCAACATCATA 60.686 45.833 13.41 0.00 0.00 2.15
943 1001 2.556622 GCCTGAAAAACGGATCCAGAAA 59.443 45.455 13.41 0.00 0.00 2.52
948 1006 1.136774 GCGCCTGAAAAACGGATCC 59.863 57.895 0.00 0.00 0.00 3.36
984 1042 0.179084 TCATCCTGCCCGACGAAATC 60.179 55.000 0.00 0.00 0.00 2.17
994 1052 1.434696 CCAATGCGTTCATCCTGCC 59.565 57.895 0.00 0.00 31.27 4.85
1142 1200 6.210796 CAGATTCACTCATTCACAGCAAAAA 58.789 36.000 0.00 0.00 0.00 1.94
1242 1340 7.948278 AGAAATAATCGCAGGTCAACTATAC 57.052 36.000 0.00 0.00 0.00 1.47
1244 1342 9.209175 GATAAGAAATAATCGCAGGTCAACTAT 57.791 33.333 0.00 0.00 0.00 2.12
1323 1447 5.929992 TGAAGTAGTAGGTTGGAAAATGTCG 59.070 40.000 0.00 0.00 0.00 4.35
1356 1480 9.100197 AGTGAAGTTCCCCACAAATAAATAAAT 57.900 29.630 0.00 0.00 35.84 1.40
1364 1488 3.909732 TCAAGTGAAGTTCCCCACAAAT 58.090 40.909 0.00 0.00 35.84 2.32
1369 1493 4.803452 AGAAAATCAAGTGAAGTTCCCCA 58.197 39.130 0.00 0.00 0.00 4.96
1371 1495 6.000840 AGAGAGAAAATCAAGTGAAGTTCCC 58.999 40.000 0.00 0.00 0.00 3.97
1373 1497 7.225538 TGTGAGAGAGAAAATCAAGTGAAGTTC 59.774 37.037 0.00 0.00 0.00 3.01
1374 1498 7.011857 GTGTGAGAGAGAAAATCAAGTGAAGTT 59.988 37.037 0.00 0.00 0.00 2.66
1392 1516 4.282195 AGGGAAAGTAAGAGTGTGTGAGAG 59.718 45.833 0.00 0.00 0.00 3.20
1401 1525 5.700402 ACATGCATAGGGAAAGTAAGAGT 57.300 39.130 0.00 0.00 0.00 3.24
1411 1535 9.812347 ATCAGAATAAATTAACATGCATAGGGA 57.188 29.630 0.00 0.00 0.00 4.20
1466 1599 2.288825 TGGCTAAGAGGTCAGTTCAACG 60.289 50.000 0.00 0.00 0.00 4.10
1476 1609 3.780626 ACAGAGTAAGTGGCTAAGAGGT 58.219 45.455 0.00 0.00 0.00 3.85
1508 1641 0.319211 TTAGAACGGTCCTGCACACG 60.319 55.000 0.00 0.00 0.00 4.49
1521 1654 8.129211 ACAGCAAACATACTCAAAAGTTAGAAC 58.871 33.333 0.00 0.00 36.92 3.01
1528 1661 7.810658 ACATAGACAGCAAACATACTCAAAAG 58.189 34.615 0.00 0.00 0.00 2.27
1541 1674 6.464222 ACAGTTTAGCTTACATAGACAGCAA 58.536 36.000 0.00 0.00 35.88 3.91
1543 1676 6.969828 AACAGTTTAGCTTACATAGACAGC 57.030 37.500 0.00 0.00 0.00 4.40
1621 1755 2.645838 ATGTCCCATCATCTTTCGGG 57.354 50.000 0.00 0.00 40.32 5.14
1736 1876 9.615660 ACAGAAGAACCCAGGAATATATATACA 57.384 33.333 0.00 0.00 0.00 2.29
1780 1938 3.623060 GCAAGAATCGAGTGCTTATTGGA 59.377 43.478 0.00 0.00 35.36 3.53
1784 1942 2.205074 CGGCAAGAATCGAGTGCTTAT 58.795 47.619 11.45 0.00 38.36 1.73
1793 1951 3.425938 GACAGCGCGGCAAGAATCG 62.426 63.158 8.83 0.00 0.00 3.34
1806 1966 0.179215 CATTTCAAGTCGGCGACAGC 60.179 55.000 37.71 15.24 44.18 4.40
1833 1993 3.121944 CGGAAGGAGATCGAATTTATGCG 59.878 47.826 0.00 0.00 0.00 4.73
1868 2028 5.334414 GGCTGAACAGTAAGTCATTCAACTG 60.334 44.000 3.77 0.00 43.90 3.16
1883 2043 3.914426 AACTAGGTATGGGCTGAACAG 57.086 47.619 0.00 0.00 0.00 3.16
1964 2124 7.804843 TCCAGTATAGTAGCTTTAGTGAGAC 57.195 40.000 0.00 0.00 0.00 3.36
2213 2383 2.997897 AGGTCTCCGGGACTGCAC 60.998 66.667 18.67 6.15 43.97 4.57
2222 2392 0.242286 CCGATATGCTCAGGTCTCCG 59.758 60.000 0.00 0.00 0.00 4.63
2249 2419 0.393820 TGAAAACTCGGGTAAGCCGT 59.606 50.000 0.00 0.00 34.97 5.68
2318 2488 0.748005 GTGCGTTGGTGCCCATATCT 60.748 55.000 0.00 0.00 31.53 1.98
2551 2722 9.328845 GGAAATAACATTTCCATTGCACATTAT 57.671 29.630 20.67 0.00 45.50 1.28
2572 2745 6.406624 GCATCTTCCACATTTGATCTGGAAAT 60.407 38.462 12.84 7.99 42.29 2.17
2582 2755 3.520290 ATGCTGCATCTTCCACATTTG 57.480 42.857 9.81 0.00 0.00 2.32
2586 2759 2.516906 TCAAATGCTGCATCTTCCACA 58.483 42.857 16.55 0.00 0.00 4.17
2820 3032 2.437651 TCACACCACACTGAATCCTCAA 59.562 45.455 0.00 0.00 0.00 3.02
2937 3150 8.999905 TTACTCCCTTTTGTAACCATAAAGTT 57.000 30.769 0.00 0.00 0.00 2.66
2964 3177 3.481453 AGAAAAGTTCTGGTCTTGCTCC 58.519 45.455 0.00 0.00 38.91 4.70
2965 3178 5.760743 AGTAAGAAAAGTTCTGGTCTTGCTC 59.239 40.000 9.06 0.00 38.24 4.26
2966 3179 5.685728 AGTAAGAAAAGTTCTGGTCTTGCT 58.314 37.500 9.06 9.06 40.59 3.91
2967 3180 7.492352 TTAGTAAGAAAAGTTCTGGTCTTGC 57.508 36.000 0.00 0.00 40.59 4.01
2970 3183 9.901172 TCTTTTTAGTAAGAAAAGTTCTGGTCT 57.099 29.630 8.61 0.00 42.13 3.85
3054 3268 1.412343 TCCCTGAAAAAGGCAAAGCAC 59.588 47.619 0.00 0.00 45.89 4.40
3058 3272 2.298729 CCGAATCCCTGAAAAAGGCAAA 59.701 45.455 0.00 0.00 45.89 3.68
3077 3292 0.748005 CCCAGGAGCCAACATTACCG 60.748 60.000 0.00 0.00 0.00 4.02
3358 3577 6.786959 AGCAGAAATCTGATAGAAGGTAGGAT 59.213 38.462 14.43 0.00 46.59 3.24
3359 3578 6.139671 AGCAGAAATCTGATAGAAGGTAGGA 58.860 40.000 14.43 0.00 46.59 2.94
3378 3597 8.972127 ACTAGTATAATTGAAGTTCAGAGCAGA 58.028 33.333 5.56 0.00 0.00 4.26
3469 3697 4.540099 TCCCTAGGAGAACAAATCATGGTT 59.460 41.667 11.48 0.00 0.00 3.67
3480 3712 2.501723 TCAGCATTGTCCCTAGGAGAAC 59.498 50.000 11.48 6.16 37.80 3.01
3517 3749 0.961753 TCGCAGCCTCGATGATGTAT 59.038 50.000 7.76 0.00 33.02 2.29
4007 4239 7.083858 TGAACTTTTTGTTGAGTTGAGACTTG 58.916 34.615 0.00 0.00 39.30 3.16
4013 4245 9.232082 CGATTATTGAACTTTTTGTTGAGTTGA 57.768 29.630 0.00 0.00 39.30 3.18
4097 4330 0.605860 AGAAGAAGGTGCTGCTGCTG 60.606 55.000 17.00 0.77 40.48 4.41
4105 4338 2.096013 GCGGATTACAAGAAGAAGGTGC 59.904 50.000 0.00 0.00 0.00 5.01
4167 4400 5.830457 TCAACACCATCAAATGTTACCAAGA 59.170 36.000 0.00 0.00 36.92 3.02
4184 4417 1.394917 GACTCACGCATCATCAACACC 59.605 52.381 0.00 0.00 0.00 4.16
4230 4469 2.180017 CGATGTTGGCTGGCTTGC 59.820 61.111 2.00 0.00 0.00 4.01
4245 4489 0.313987 ACTCACGCAGTTCATGACGA 59.686 50.000 10.08 0.00 41.61 4.20
4261 4505 1.226717 GCGACCCACTCATCGACTC 60.227 63.158 0.00 0.00 40.86 3.36
4279 4523 2.808315 CCTCATCTCCACCGACGG 59.192 66.667 13.61 13.61 0.00 4.79
4652 4896 2.606826 GGGTCCACTTCTCCCCGT 60.607 66.667 0.00 0.00 35.52 5.28
4741 4997 4.790861 GTTCGACCTCCCCGACGC 62.791 72.222 0.00 0.00 35.61 5.19
4742 4998 4.471726 CGTTCGACCTCCCCGACG 62.472 72.222 0.00 0.00 35.61 5.12
4743 4999 4.125695 CCGTTCGACCTCCCCGAC 62.126 72.222 0.00 0.00 35.61 4.79
4862 5118 2.747822 GCTCGCCGTGACTCTCGTA 61.748 63.158 0.00 0.00 0.00 3.43
4880 5137 1.359475 GAGGTAGGTAAGCCGCTCG 59.641 63.158 0.00 0.00 40.50 5.03
4884 5141 1.614413 GAGGATGAGGTAGGTAAGCCG 59.386 57.143 0.00 0.00 40.50 5.52
4923 5180 4.208686 GGCTTCGTCTCCGGCGAT 62.209 66.667 9.30 0.00 38.21 4.58


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

AutoCloner maintained by Alex Coulton.