Multiple sequence alignment - TraesCS3B01G379200

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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 TraesCS3B01G379200 chr3B 100.000 4061 0 0 1 4061 597086924 597090984 0.000000e+00 7500.0
1 TraesCS3B01G379200 chr3B 100.000 50 0 0 4303 4352 597091226 597091275 4.630000e-15 93.5
2 TraesCS3B01G379200 chr3B 84.211 95 12 1 3491 3585 372246297 372246388 5.990000e-14 89.8
3 TraesCS3B01G379200 chr3D 92.947 3516 175 32 1 3490 454507433 454510901 0.000000e+00 5051.0
4 TraesCS3B01G379200 chr3D 79.714 419 44 15 3572 3957 454510897 454511307 9.280000e-67 265.0
5 TraesCS3B01G379200 chr3D 84.746 59 7 2 2739 2796 337974306 337974249 1.690000e-04 58.4
6 TraesCS3B01G379200 chr3A 92.996 3027 138 36 470 3476 596513312 596516284 0.000000e+00 4348.0
7 TraesCS3B01G379200 chr3A 91.803 427 19 7 1 424 596512886 596513299 8.110000e-162 580.0
8 TraesCS3B01G379200 chr3A 91.386 267 20 2 3230 3494 596546559 596546824 3.200000e-96 363.0
9 TraesCS3B01G379200 chr3A 85.333 300 20 12 3532 3830 596546821 596547097 5.510000e-74 289.0
10 TraesCS3B01G379200 chr1D 89.498 219 22 1 2015 2233 391862166 391862383 4.290000e-70 276.0
11 TraesCS3B01G379200 chr1D 95.161 124 6 0 2567 2690 391862608 391862731 3.430000e-46 196.0
12 TraesCS3B01G379200 chr1D 87.770 139 17 0 2692 2830 391862835 391862973 3.480000e-36 163.0
13 TraesCS3B01G379200 chr1D 92.424 66 5 0 2602 2667 436713086 436713021 1.290000e-15 95.3
14 TraesCS3B01G379200 chr1D 87.879 66 8 0 2646 2711 53380913 53380848 1.300000e-10 78.7
15 TraesCS3B01G379200 chr1B 89.498 219 22 1 2015 2233 530779787 530779570 4.290000e-70 276.0
16 TraesCS3B01G379200 chr1B 92.126 127 10 0 2567 2693 530779345 530779219 3.460000e-41 180.0
17 TraesCS3B01G379200 chr1B 88.489 139 16 0 2692 2830 530779119 530778981 7.490000e-38 169.0
18 TraesCS3B01G379200 chr1B 90.541 74 7 0 3491 3564 598882800 598882727 9.960000e-17 99.0
19 TraesCS3B01G379200 chr1B 92.424 66 5 0 2602 2667 591512506 591512441 1.290000e-15 95.3
20 TraesCS3B01G379200 chr1B 85.556 90 11 2 3476 3564 675980654 675980566 4.630000e-15 93.5
21 TraesCS3B01G379200 chr1B 89.394 66 7 0 2646 2711 87732757 87732692 2.790000e-12 84.2
22 TraesCS3B01G379200 chr1A 89.041 219 23 1 2015 2233 493502007 493501790 1.990000e-68 270.0
23 TraesCS3B01G379200 chr1A 86.331 139 19 0 2692 2830 493501339 493501201 7.540000e-33 152.0
24 TraesCS3B01G379200 chr1A 92.424 66 5 0 2602 2667 533742350 533742285 1.290000e-15 95.3
25 TraesCS3B01G379200 chr1A 84.946 93 9 4 3474 3564 550630442 550630531 5.990000e-14 89.8
26 TraesCS3B01G379200 chr2B 88.060 134 11 5 2689 2819 500590533 500590402 2.100000e-33 154.0
27 TraesCS3B01G379200 chr2A 88.462 130 11 4 2692 2819 562984727 562984854 2.100000e-33 154.0
28 TraesCS3B01G379200 chr2A 89.157 83 9 0 3482 3564 646552417 646552499 2.140000e-18 104.0
29 TraesCS3B01G379200 chr2A 89.744 78 8 0 3487 3564 694455296 694455373 2.770000e-17 100.0
30 TraesCS3B01G379200 chr2D 88.889 126 8 6 2689 2811 425216117 425215995 2.710000e-32 150.0
31 TraesCS3B01G379200 chr7B 90.541 74 7 0 3491 3564 680211606 680211533 9.960000e-17 99.0
32 TraesCS3B01G379200 chr7A 90.541 74 7 0 3491 3564 692919273 692919200 9.960000e-17 99.0
33 TraesCS3B01G379200 chr6B 90.541 74 7 0 3491 3564 458503568 458503495 9.960000e-17 99.0
34 TraesCS3B01G379200 chr5D 75.904 166 38 2 2029 2193 472237771 472237935 2.790000e-12 84.2
35 TraesCS3B01G379200 chr5B 75.904 166 38 2 2029 2193 578540649 578540813 2.790000e-12 84.2
36 TraesCS3B01G379200 chr5A 75.610 164 38 2 2031 2193 591443768 591443930 3.610000e-11 80.5


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 TraesCS3B01G379200 chr3B 597086924 597091275 4351 False 3796.750000 7500 100.000000 1 4352 2 chr3B.!!$F2 4351
1 TraesCS3B01G379200 chr3D 454507433 454511307 3874 False 2658.000000 5051 86.330500 1 3957 2 chr3D.!!$F1 3956
2 TraesCS3B01G379200 chr3A 596512886 596516284 3398 False 2464.000000 4348 92.399500 1 3476 2 chr3A.!!$F1 3475
3 TraesCS3B01G379200 chr3A 596546559 596547097 538 False 326.000000 363 88.359500 3230 3830 2 chr3A.!!$F2 600
4 TraesCS3B01G379200 chr1D 391862166 391862973 807 False 211.666667 276 90.809667 2015 2830 3 chr1D.!!$F1 815
5 TraesCS3B01G379200 chr1B 530778981 530779787 806 True 208.333333 276 90.037667 2015 2830 3 chr1B.!!$R5 815
6 TraesCS3B01G379200 chr1A 493501201 493502007 806 True 211.000000 270 87.686000 2015 2830 2 chr1A.!!$R2 815

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
431 435 0.319405 AAGGCAGCCAAGCAAACATC 59.681 50.0 15.80 0.0 35.83 3.06 F
661 665 0.326264 GAGCCATGACCACCAACTCT 59.674 55.0 0.00 0.0 0.00 3.24 F
940 944 0.478507 CCTCCTCCTCCTCCTCTCTC 59.521 65.0 0.00 0.0 0.00 3.20 F
1308 1312 0.950555 CTCCAGTGTAAGCAAGCGCA 60.951 55.0 11.47 0.0 42.27 6.09 F
3077 3228 0.745845 GTACATGAGCCAGCACCAGG 60.746 60.0 0.00 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1357 1366 0.747852 ACCAACCAAAACCGCGAATT 59.252 45.000 8.23 0.0 0.00 2.17 R
2511 2548 0.532115 CCTCCTGAAAATTTGGCCGG 59.468 55.000 0.00 0.0 0.00 6.13 R
2557 2594 3.679738 CGGTTGCCGGCCATGTTT 61.680 61.111 26.77 0.0 44.15 2.83 R
3294 3447 1.007387 GAACCCTTTTGTGCAGCCG 60.007 57.895 0.00 0.0 0.00 5.52 R
3966 4197 0.037232 CGAAGTGGGAGGAGTGGTTC 60.037 60.000 0.00 0.0 0.00 3.62 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
40 41 7.752638 ACCACTCCTACCAAAGTAGTTTAATT 58.247 34.615 0.00 0.00 43.92 1.40
103 104 7.407337 GTCAGCAAGTAGAATTATTTAACCCG 58.593 38.462 0.00 0.00 0.00 5.28
104 105 6.037830 TCAGCAAGTAGAATTATTTAACCCGC 59.962 38.462 0.00 0.00 0.00 6.13
105 106 5.883673 AGCAAGTAGAATTATTTAACCCGCA 59.116 36.000 0.00 0.00 0.00 5.69
106 107 6.546034 AGCAAGTAGAATTATTTAACCCGCAT 59.454 34.615 0.00 0.00 0.00 4.73
107 108 6.856426 GCAAGTAGAATTATTTAACCCGCATC 59.144 38.462 0.00 0.00 0.00 3.91
152 156 2.534042 TGGGTCCTGGTTGAAACAAA 57.466 45.000 0.00 0.00 0.00 2.83
253 257 9.248291 CATTATTTGAAAATTCTACCGAATGGG 57.752 33.333 0.00 0.00 39.72 4.00
260 264 6.635030 AAATTCTACCGAATGGGCTATTTC 57.365 37.500 0.00 0.00 39.72 2.17
268 272 2.348411 ATGGGCTATTTCCCTTCGTG 57.652 50.000 0.12 0.00 46.67 4.35
319 323 7.679659 AAGATACTTTTCGAAGTTTGTTTGC 57.320 32.000 0.00 0.00 34.37 3.68
330 334 5.052633 CGAAGTTTGTTTGCGTTTCTAAAGG 60.053 40.000 0.00 0.00 0.00 3.11
385 389 8.853077 TCAGTGATCAGAGTATGAACAAAAAT 57.147 30.769 0.00 0.00 41.78 1.82
428 432 0.939419 CAAAAGGCAGCCAAGCAAAC 59.061 50.000 15.80 0.00 35.83 2.93
429 433 0.540923 AAAAGGCAGCCAAGCAAACA 59.459 45.000 15.80 0.00 35.83 2.83
431 435 0.319405 AAGGCAGCCAAGCAAACATC 59.681 50.000 15.80 0.00 35.83 3.06
433 437 1.444895 GCAGCCAAGCAAACATCGG 60.445 57.895 0.00 0.00 0.00 4.18
435 439 0.387622 CAGCCAAGCAAACATCGGTG 60.388 55.000 0.00 0.00 0.00 4.94
436 440 0.823356 AGCCAAGCAAACATCGGTGT 60.823 50.000 0.00 0.00 41.28 4.16
444 448 3.927555 AACATCGGTGTTGATCCGT 57.072 47.368 14.50 0.00 46.43 4.69
464 468 1.747709 ATGGACATGACAAGCTCAGC 58.252 50.000 0.00 0.00 30.20 4.26
465 469 0.397564 TGGACATGACAAGCTCAGCA 59.602 50.000 0.00 0.00 30.20 4.41
475 479 3.185155 GCTCAGCAGCACCACATC 58.815 61.111 0.00 0.00 46.06 3.06
477 481 1.367599 GCTCAGCAGCACCACATCTC 61.368 60.000 0.00 0.00 46.06 2.75
485 489 3.519579 CAGCACCACATCTCTACAAGAG 58.480 50.000 0.00 0.00 43.64 2.85
489 493 3.869832 CACCACATCTCTACAAGAGCATG 59.130 47.826 0.00 6.86 42.04 4.06
502 506 2.649831 AGCATGGCTCCAAACAGTG 58.350 52.632 0.00 0.00 30.62 3.66
507 511 1.909700 TGGCTCCAAACAGTGAATCC 58.090 50.000 0.00 0.00 0.00 3.01
518 522 1.590238 CAGTGAATCCGATCGAAGCAC 59.410 52.381 18.66 17.50 0.00 4.40
542 546 8.635124 CACCATAATTAAACTAGTTTTGCGTTG 58.365 33.333 25.07 16.44 34.23 4.10
546 550 9.738832 ATAATTAAACTAGTTTTGCGTTGTGTT 57.261 25.926 25.07 9.87 34.23 3.32
563 567 6.857964 CGTTGTGTTTCTTAGCTTCAATCATT 59.142 34.615 0.00 0.00 0.00 2.57
564 568 7.379529 CGTTGTGTTTCTTAGCTTCAATCATTT 59.620 33.333 0.00 0.00 0.00 2.32
565 569 8.694394 GTTGTGTTTCTTAGCTTCAATCATTTC 58.306 33.333 0.00 0.00 0.00 2.17
600 604 8.726988 CGACCTCAATTCTAATTTAGAACCAAA 58.273 33.333 18.65 6.61 46.58 3.28
648 652 3.771216 ACAGGTCAAAGAAATGAGCCAT 58.229 40.909 3.14 0.00 46.41 4.40
661 665 0.326264 GAGCCATGACCACCAACTCT 59.674 55.000 0.00 0.00 0.00 3.24
677 681 3.197927 ACTCTTCCTCTCACCCAGAAT 57.802 47.619 0.00 0.00 0.00 2.40
938 942 1.152546 GCCTCCTCCTCCTCCTCTC 60.153 68.421 0.00 0.00 0.00 3.20
939 943 1.655114 GCCTCCTCCTCCTCCTCTCT 61.655 65.000 0.00 0.00 0.00 3.10
940 944 0.478507 CCTCCTCCTCCTCCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
941 945 0.478507 CTCCTCCTCCTCCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
1005 1009 2.175566 CCGTCGTACGCCGTAACA 59.824 61.111 17.94 0.00 40.91 2.41
1007 1011 2.479782 CGTCGTACGCCGTAACACG 61.480 63.158 11.00 9.66 35.23 4.49
1046 1050 1.282157 TCAGAGTCCTCTCCGATGACA 59.718 52.381 0.00 0.00 41.26 3.58
1217 1221 2.202610 TCGCCTTCGCTCATGTCG 60.203 61.111 0.00 0.00 35.26 4.35
1308 1312 0.950555 CTCCAGTGTAAGCAAGCGCA 60.951 55.000 11.47 0.00 42.27 6.09
1357 1366 2.159352 TCCGATTGAATTCGTGTCGCTA 60.159 45.455 16.68 8.04 37.42 4.26
1604 1619 1.664965 GTGGCGTCACAGGTGAGAC 60.665 63.158 16.80 0.00 43.13 3.36
1618 1633 2.740714 GAGACCACGAACCATGCGC 61.741 63.158 0.00 0.00 0.00 6.09
1627 1642 3.958147 AACCATGCGCTGTCCTCGG 62.958 63.158 9.73 0.70 0.00 4.63
1669 1684 9.947669 AGTATAAACTACTTGCACTAGAATACG 57.052 33.333 0.00 0.00 32.84 3.06
1733 1748 3.681897 GCTGTCGTGTCATCATCTTTTCT 59.318 43.478 0.00 0.00 0.00 2.52
1764 1779 6.380079 AAGATGGTTGTGAGAAATAGTCCT 57.620 37.500 0.00 0.00 0.00 3.85
1769 1785 4.691216 GGTTGTGAGAAATAGTCCTGTGAC 59.309 45.833 0.00 0.00 42.09 3.67
1799 1815 2.058125 TAGCGGAAACCCCAACAGCA 62.058 55.000 0.00 0.00 34.14 4.41
1853 1869 1.063717 GCAATGATTCAGGGGGAGGAA 60.064 52.381 0.00 0.00 0.00 3.36
1911 1936 1.250328 CCAGCAACAAGAAGGCATGA 58.750 50.000 0.00 0.00 0.00 3.07
2257 2282 4.437587 GGCCCAGGTGCTGCAGAT 62.438 66.667 20.43 0.00 0.00 2.90
2440 2477 6.296365 GGTACCAACTTCAACTTGTACTTC 57.704 41.667 7.15 0.00 0.00 3.01
2441 2478 5.050567 GGTACCAACTTCAACTTGTACTTCG 60.051 44.000 7.15 0.00 0.00 3.79
2442 2479 4.761975 ACCAACTTCAACTTGTACTTCGA 58.238 39.130 0.00 0.00 0.00 3.71
2447 2484 7.700656 CCAACTTCAACTTGTACTTCGATTTTT 59.299 33.333 0.00 0.00 0.00 1.94
2448 2485 8.734030 CAACTTCAACTTGTACTTCGATTTTTC 58.266 33.333 0.00 0.00 0.00 2.29
2449 2486 8.209917 ACTTCAACTTGTACTTCGATTTTTCT 57.790 30.769 0.00 0.00 0.00 2.52
2450 2487 8.122952 ACTTCAACTTGTACTTCGATTTTTCTG 58.877 33.333 0.00 0.00 0.00 3.02
2451 2488 6.954944 TCAACTTGTACTTCGATTTTTCTGG 58.045 36.000 0.00 0.00 0.00 3.86
2452 2489 6.764085 TCAACTTGTACTTCGATTTTTCTGGA 59.236 34.615 0.00 0.00 0.00 3.86
2453 2490 7.444183 TCAACTTGTACTTCGATTTTTCTGGAT 59.556 33.333 0.00 0.00 0.00 3.41
2454 2491 7.365840 ACTTGTACTTCGATTTTTCTGGATC 57.634 36.000 0.00 0.00 0.00 3.36
2455 2492 6.371825 ACTTGTACTTCGATTTTTCTGGATCC 59.628 38.462 4.20 4.20 0.00 3.36
2456 2493 5.800296 TGTACTTCGATTTTTCTGGATCCA 58.200 37.500 15.27 15.27 0.00 3.41
2457 2494 6.234920 TGTACTTCGATTTTTCTGGATCCAA 58.765 36.000 17.00 0.00 0.00 3.53
2458 2495 5.629079 ACTTCGATTTTTCTGGATCCAAC 57.371 39.130 17.00 1.03 0.00 3.77
2459 2496 4.154195 ACTTCGATTTTTCTGGATCCAACG 59.846 41.667 17.00 5.17 0.00 4.10
2463 2500 4.390603 CGATTTTTCTGGATCCAACGTGTA 59.609 41.667 17.00 0.22 0.00 2.90
2481 2518 5.231357 ACGTGTATATGTACGAGTTGCATTG 59.769 40.000 17.03 0.00 42.54 2.82
2511 2548 5.354513 GGAACAGAGGAAATTAACCTGCTAC 59.645 44.000 8.55 0.00 37.93 3.58
2557 2594 1.683025 TGGTGACGGCGAGGGAATA 60.683 57.895 16.62 0.00 0.00 1.75
2575 2615 4.966787 AACATGGCCGGCAACCGT 62.967 61.111 30.85 15.90 46.80 4.83
3015 3166 2.887889 CGTTCGGCTTCAACGGCAA 61.888 57.895 7.27 0.00 42.36 4.52
3077 3228 0.745845 GTACATGAGCCAGCACCAGG 60.746 60.000 0.00 0.00 0.00 4.45
3175 3326 1.349067 ACTCCCAGTACTGACCAACC 58.651 55.000 24.68 0.00 0.00 3.77
3194 3345 2.624838 ACCAGTGTCAGAAATGGCAAAG 59.375 45.455 0.00 0.00 36.21 2.77
3218 3369 3.119101 ACACGACGAGATGGAGCTTTATT 60.119 43.478 0.00 0.00 0.00 1.40
3219 3370 4.097437 ACACGACGAGATGGAGCTTTATTA 59.903 41.667 0.00 0.00 0.00 0.98
3221 3372 5.343593 CACGACGAGATGGAGCTTTATTATC 59.656 44.000 0.00 0.00 0.00 1.75
3222 3373 5.009710 ACGACGAGATGGAGCTTTATTATCA 59.990 40.000 0.00 0.00 0.00 2.15
3223 3374 6.096036 CGACGAGATGGAGCTTTATTATCAT 58.904 40.000 0.00 0.00 0.00 2.45
3224 3375 6.034363 CGACGAGATGGAGCTTTATTATCATG 59.966 42.308 0.00 0.00 0.00 3.07
3294 3447 1.448013 GAGGCCCGTAGTTGCAGAC 60.448 63.158 0.00 0.00 0.00 3.51
3310 3464 2.123897 ACGGCTGCACAAAAGGGT 60.124 55.556 0.50 0.00 0.00 4.34
3318 3472 1.063266 TGCACAAAAGGGTTCCCTTCT 60.063 47.619 21.57 7.11 44.85 2.85
3321 3475 3.118408 GCACAAAAGGGTTCCCTTCTTTT 60.118 43.478 21.57 11.06 44.85 2.27
3440 3595 8.632679 ACACAGAAGTATGTTGTTGAATTCAAT 58.367 29.630 23.05 9.97 38.24 2.57
3482 3637 9.868277 AAATTTGTCACTATTCAAGTTTCACAA 57.132 25.926 0.00 0.00 35.76 3.33
3485 3640 7.566760 TGTCACTATTCAAGTTTCACAATGT 57.433 32.000 0.00 0.00 35.76 2.71
3486 3641 7.416817 TGTCACTATTCAAGTTTCACAATGTG 58.583 34.615 7.12 7.12 35.76 3.21
3487 3642 7.281999 TGTCACTATTCAAGTTTCACAATGTGA 59.718 33.333 12.63 12.63 37.24 3.58
3500 3655 7.864108 TTCACAATGTGAATTACTCCCATAG 57.136 36.000 23.28 0.00 45.88 2.23
3501 3656 6.957631 TCACAATGTGAATTACTCCCATAGT 58.042 36.000 14.37 0.00 39.78 2.12
3502 3657 8.084985 TCACAATGTGAATTACTCCCATAGTA 57.915 34.615 14.37 0.00 39.78 1.82
3503 3658 8.544622 TCACAATGTGAATTACTCCCATAGTAA 58.455 33.333 14.37 0.47 44.19 2.24
3504 3659 9.173021 CACAATGTGAATTACTCCCATAGTAAA 57.827 33.333 7.78 0.00 43.33 2.01
3537 3692 8.854614 AAGAGCATTTAAATCACTGAACTAGT 57.145 30.769 0.00 0.00 41.36 2.57
3538 3693 9.944376 AAGAGCATTTAAATCACTGAACTAGTA 57.056 29.630 0.00 0.00 37.60 1.82
3539 3694 9.944376 AGAGCATTTAAATCACTGAACTAGTAA 57.056 29.630 0.00 0.00 37.60 2.24
3550 3705 9.757227 ATCACTGAACTAGTAATCTAAATGCTC 57.243 33.333 0.00 0.00 37.60 4.26
3551 3706 8.972127 TCACTGAACTAGTAATCTAAATGCTCT 58.028 33.333 0.00 0.00 37.60 4.09
3552 3707 9.593134 CACTGAACTAGTAATCTAAATGCTCTT 57.407 33.333 0.00 0.00 37.60 2.85
3605 3803 7.504403 AGATAGTGGTATGTTTCATTCTCAGG 58.496 38.462 0.00 0.00 0.00 3.86
3606 3804 5.762179 AGTGGTATGTTTCATTCTCAGGA 57.238 39.130 0.00 0.00 0.00 3.86
3608 3806 6.542821 AGTGGTATGTTTCATTCTCAGGAAA 58.457 36.000 0.00 0.00 34.90 3.13
3615 3813 8.641498 ATGTTTCATTCTCAGGAAAAGTGTAT 57.359 30.769 0.00 0.00 35.03 2.29
3633 3831 5.825679 AGTGTATCAGACCTCAGATGTACTC 59.174 44.000 0.00 0.00 0.00 2.59
3635 3833 5.590663 TGTATCAGACCTCAGATGTACTCAC 59.409 44.000 0.00 0.00 0.00 3.51
3646 3852 5.046529 CAGATGTACTCACTGTAATCCAGC 58.953 45.833 0.00 0.00 45.68 4.85
3656 3862 5.414454 TCACTGTAATCCAGCCATTTTGTAC 59.586 40.000 0.00 0.00 45.68 2.90
3790 4004 0.395724 AAAATCGGCCCTCCCACATC 60.396 55.000 0.00 0.00 0.00 3.06
3813 4027 4.384868 CCCGAACTAACCATCCATTTAGGT 60.385 45.833 0.00 0.00 39.02 3.08
3817 4031 7.501225 CCGAACTAACCATCCATTTAGGTATTT 59.499 37.037 0.00 0.00 39.02 1.40
3831 4062 1.049402 GTATTTCTCTCCCTCCCCGG 58.951 60.000 0.00 0.00 0.00 5.73
3841 4072 2.535331 CCTCCCCGGGGTTTTCACT 61.535 63.158 38.73 0.00 36.47 3.41
3846 4077 0.688487 CCCGGGGTTTTCACTGACTA 59.312 55.000 14.71 0.00 0.00 2.59
3847 4078 1.072648 CCCGGGGTTTTCACTGACTAA 59.927 52.381 14.71 0.00 0.00 2.24
3849 4080 2.812011 CCGGGGTTTTCACTGACTAAAG 59.188 50.000 0.00 0.00 0.00 1.85
3861 4092 4.213270 CACTGACTAAAGCGATTTTGACCA 59.787 41.667 14.24 9.97 0.00 4.02
3873 4104 0.184692 TTTGACCATGGTGACTGCCA 59.815 50.000 25.52 10.15 43.48 4.92
3887 4118 2.440247 GCCAAGTTAGCCCGCCAT 60.440 61.111 0.00 0.00 0.00 4.40
3892 4123 2.753849 GTTAGCCCGCCATGCCAA 60.754 61.111 0.00 0.00 0.00 4.52
3906 4137 3.119029 CCATGCCAACTCTTTAATGTGGG 60.119 47.826 0.00 0.00 0.00 4.61
3910 4141 3.089284 CCAACTCTTTAATGTGGGACCC 58.911 50.000 2.45 2.45 28.78 4.46
3911 4142 3.499563 CCAACTCTTTAATGTGGGACCCA 60.500 47.826 9.95 9.95 28.78 4.51
3912 4143 3.721087 ACTCTTTAATGTGGGACCCAG 57.279 47.619 15.52 0.00 32.34 4.45
3913 4144 2.290960 ACTCTTTAATGTGGGACCCAGC 60.291 50.000 15.52 9.81 32.34 4.85
3914 4145 1.992557 TCTTTAATGTGGGACCCAGCT 59.007 47.619 15.52 3.61 32.34 4.24
3915 4146 3.186283 TCTTTAATGTGGGACCCAGCTA 58.814 45.455 15.52 3.72 32.34 3.32
3916 4147 3.589735 TCTTTAATGTGGGACCCAGCTAA 59.410 43.478 15.52 9.03 32.34 3.09
3917 4148 3.359695 TTAATGTGGGACCCAGCTAAC 57.640 47.619 15.52 1.63 32.34 2.34
3918 4149 0.035439 AATGTGGGACCCAGCTAACG 60.035 55.000 15.52 0.00 32.34 3.18
3923 4154 1.078426 GGACCCAGCTAACGCACAT 60.078 57.895 0.00 0.00 39.10 3.21
3928 4159 1.867233 CCCAGCTAACGCACATATCAC 59.133 52.381 0.00 0.00 39.10 3.06
3938 4169 2.009774 GCACATATCACACACCTCCAC 58.990 52.381 0.00 0.00 0.00 4.02
3939 4170 2.632377 CACATATCACACACCTCCACC 58.368 52.381 0.00 0.00 0.00 4.61
3950 4181 2.747855 CTCCACCGCTTCTTGCCC 60.748 66.667 0.00 0.00 38.78 5.36
3959 4190 4.634703 TTCTTGCCCGCTCCGCAA 62.635 61.111 0.00 0.00 43.71 4.85
3967 4198 4.717629 CGCTCCGCAACCACGAGA 62.718 66.667 0.00 0.00 34.06 4.04
3968 4199 2.357034 GCTCCGCAACCACGAGAA 60.357 61.111 0.00 0.00 34.06 2.87
3969 4200 2.668280 GCTCCGCAACCACGAGAAC 61.668 63.158 0.00 0.00 34.06 3.01
3970 4201 2.027625 CTCCGCAACCACGAGAACC 61.028 63.158 0.00 0.00 34.06 3.62
3971 4202 2.280524 CCGCAACCACGAGAACCA 60.281 61.111 0.00 0.00 34.06 3.67
3972 4203 2.604174 CCGCAACCACGAGAACCAC 61.604 63.158 0.00 0.00 34.06 4.16
3973 4204 1.594293 CGCAACCACGAGAACCACT 60.594 57.895 0.00 0.00 34.06 4.00
3974 4205 1.557443 CGCAACCACGAGAACCACTC 61.557 60.000 0.00 0.00 41.79 3.51
3975 4206 1.228657 GCAACCACGAGAACCACTCC 61.229 60.000 0.00 0.00 42.18 3.85
3976 4207 0.393077 CAACCACGAGAACCACTCCT 59.607 55.000 0.00 0.00 42.18 3.69
3977 4208 0.680061 AACCACGAGAACCACTCCTC 59.320 55.000 0.00 0.00 42.18 3.71
3978 4209 1.186267 ACCACGAGAACCACTCCTCC 61.186 60.000 0.00 0.00 42.18 4.30
3979 4210 1.592223 CACGAGAACCACTCCTCCC 59.408 63.158 0.00 0.00 42.18 4.30
3980 4211 1.155390 ACGAGAACCACTCCTCCCA 59.845 57.895 0.00 0.00 42.18 4.37
3981 4212 1.186267 ACGAGAACCACTCCTCCCAC 61.186 60.000 0.00 0.00 42.18 4.61
3982 4213 0.900647 CGAGAACCACTCCTCCCACT 60.901 60.000 0.00 0.00 42.18 4.00
3983 4214 1.353091 GAGAACCACTCCTCCCACTT 58.647 55.000 0.00 0.00 39.53 3.16
3984 4215 1.276705 GAGAACCACTCCTCCCACTTC 59.723 57.143 0.00 0.00 39.53 3.01
3985 4216 0.037232 GAACCACTCCTCCCACTTCG 60.037 60.000 0.00 0.00 0.00 3.79
3986 4217 0.763223 AACCACTCCTCCCACTTCGT 60.763 55.000 0.00 0.00 0.00 3.85
3987 4218 1.186267 ACCACTCCTCCCACTTCGTC 61.186 60.000 0.00 0.00 0.00 4.20
3988 4219 1.185618 CCACTCCTCCCACTTCGTCA 61.186 60.000 0.00 0.00 0.00 4.35
3989 4220 0.038159 CACTCCTCCCACTTCGTCAC 60.038 60.000 0.00 0.00 0.00 3.67
3990 4221 1.186267 ACTCCTCCCACTTCGTCACC 61.186 60.000 0.00 0.00 0.00 4.02
3991 4222 1.152419 TCCTCCCACTTCGTCACCA 60.152 57.895 0.00 0.00 0.00 4.17
3992 4223 1.004918 CCTCCCACTTCGTCACCAC 60.005 63.158 0.00 0.00 0.00 4.16
3993 4224 1.004918 CTCCCACTTCGTCACCACC 60.005 63.158 0.00 0.00 0.00 4.61
3994 4225 2.032071 CCCACTTCGTCACCACCC 59.968 66.667 0.00 0.00 0.00 4.61
3995 4226 2.813726 CCCACTTCGTCACCACCCA 61.814 63.158 0.00 0.00 0.00 4.51
3996 4227 1.147376 CCACTTCGTCACCACCCAA 59.853 57.895 0.00 0.00 0.00 4.12
3997 4228 0.464735 CCACTTCGTCACCACCCAAA 60.465 55.000 0.00 0.00 0.00 3.28
3998 4229 0.661020 CACTTCGTCACCACCCAAAC 59.339 55.000 0.00 0.00 0.00 2.93
3999 4230 0.464916 ACTTCGTCACCACCCAAACC 60.465 55.000 0.00 0.00 0.00 3.27
4000 4231 1.152922 TTCGTCACCACCCAAACCC 60.153 57.895 0.00 0.00 0.00 4.11
4001 4232 2.596338 CGTCACCACCCAAACCCC 60.596 66.667 0.00 0.00 0.00 4.95
4002 4233 2.604152 GTCACCACCCAAACCCCA 59.396 61.111 0.00 0.00 0.00 4.96
4003 4234 1.830847 GTCACCACCCAAACCCCAC 60.831 63.158 0.00 0.00 0.00 4.61
4004 4235 2.523168 CACCACCCAAACCCCACC 60.523 66.667 0.00 0.00 0.00 4.61
4005 4236 2.702253 ACCACCCAAACCCCACCT 60.702 61.111 0.00 0.00 0.00 4.00
4006 4237 2.329399 ACCACCCAAACCCCACCTT 61.329 57.895 0.00 0.00 0.00 3.50
4007 4238 1.533033 CCACCCAAACCCCACCTTC 60.533 63.158 0.00 0.00 0.00 3.46
4008 4239 1.533033 CACCCAAACCCCACCTTCC 60.533 63.158 0.00 0.00 0.00 3.46
4009 4240 2.119611 CCCAAACCCCACCTTCCC 59.880 66.667 0.00 0.00 0.00 3.97
4010 4241 2.784654 CCCAAACCCCACCTTCCCA 61.785 63.158 0.00 0.00 0.00 4.37
4011 4242 1.234529 CCAAACCCCACCTTCCCAA 59.765 57.895 0.00 0.00 0.00 4.12
4012 4243 1.118965 CCAAACCCCACCTTCCCAAC 61.119 60.000 0.00 0.00 0.00 3.77
4013 4244 1.118965 CAAACCCCACCTTCCCAACC 61.119 60.000 0.00 0.00 0.00 3.77
4014 4245 1.595058 AAACCCCACCTTCCCAACCA 61.595 55.000 0.00 0.00 0.00 3.67
4015 4246 2.117423 CCCCACCTTCCCAACCAC 59.883 66.667 0.00 0.00 0.00 4.16
4016 4247 2.117423 CCCACCTTCCCAACCACC 59.883 66.667 0.00 0.00 0.00 4.61
4017 4248 2.469765 CCCACCTTCCCAACCACCT 61.470 63.158 0.00 0.00 0.00 4.00
4018 4249 1.228552 CCACCTTCCCAACCACCTG 60.229 63.158 0.00 0.00 0.00 4.00
4019 4250 1.715019 CCACCTTCCCAACCACCTGA 61.715 60.000 0.00 0.00 0.00 3.86
4020 4251 0.250901 CACCTTCCCAACCACCTGAG 60.251 60.000 0.00 0.00 0.00 3.35
4021 4252 0.697854 ACCTTCCCAACCACCTGAGT 60.698 55.000 0.00 0.00 0.00 3.41
4022 4253 0.478507 CCTTCCCAACCACCTGAGTT 59.521 55.000 0.00 0.00 0.00 3.01
4023 4254 1.609208 CTTCCCAACCACCTGAGTTG 58.391 55.000 0.00 0.00 43.41 3.16
4024 4255 1.142870 CTTCCCAACCACCTGAGTTGA 59.857 52.381 5.25 0.00 46.03 3.18
4025 4256 1.444933 TCCCAACCACCTGAGTTGAT 58.555 50.000 5.25 0.00 46.03 2.57
4026 4257 1.073763 TCCCAACCACCTGAGTTGATG 59.926 52.381 5.25 0.00 46.03 3.07
4027 4258 1.202927 CCCAACCACCTGAGTTGATGT 60.203 52.381 5.25 0.00 46.03 3.06
4028 4259 2.154462 CCAACCACCTGAGTTGATGTC 58.846 52.381 5.25 0.00 46.03 3.06
4029 4260 1.800586 CAACCACCTGAGTTGATGTCG 59.199 52.381 0.00 0.00 46.03 4.35
4030 4261 0.320771 ACCACCTGAGTTGATGTCGC 60.321 55.000 0.00 0.00 0.00 5.19
4031 4262 0.320683 CCACCTGAGTTGATGTCGCA 60.321 55.000 0.00 0.00 0.00 5.10
4032 4263 0.792640 CACCTGAGTTGATGTCGCAC 59.207 55.000 0.00 0.00 0.00 5.34
4033 4264 0.392706 ACCTGAGTTGATGTCGCACA 59.607 50.000 0.00 0.00 0.00 4.57
4034 4265 1.002430 ACCTGAGTTGATGTCGCACAT 59.998 47.619 2.02 2.02 42.43 3.21
4035 4266 1.395954 CCTGAGTTGATGTCGCACATG 59.604 52.381 6.52 0.00 39.27 3.21
4036 4267 2.071540 CTGAGTTGATGTCGCACATGT 58.928 47.619 6.52 0.00 39.27 3.21
4037 4268 1.799994 TGAGTTGATGTCGCACATGTG 59.200 47.619 21.83 21.83 39.27 3.21
4047 4278 2.747460 CACATGTGCCCTGGACCG 60.747 66.667 13.94 0.00 0.00 4.79
4048 4279 3.249189 ACATGTGCCCTGGACCGT 61.249 61.111 0.00 0.00 0.00 4.83
4049 4280 2.034066 CATGTGCCCTGGACCGTT 59.966 61.111 0.00 0.00 0.00 4.44
4050 4281 2.034066 ATGTGCCCTGGACCGTTG 59.966 61.111 0.00 0.00 0.00 4.10
4051 4282 2.829384 ATGTGCCCTGGACCGTTGT 61.829 57.895 0.00 0.00 0.00 3.32
4052 4283 2.978010 GTGCCCTGGACCGTTGTG 60.978 66.667 0.00 0.00 0.00 3.33
4053 4284 4.947147 TGCCCTGGACCGTTGTGC 62.947 66.667 0.00 0.00 0.00 4.57
4056 4287 4.619227 CCTGGACCGTTGTGCCGT 62.619 66.667 0.00 0.00 30.59 5.68
4057 4288 3.345808 CTGGACCGTTGTGCCGTG 61.346 66.667 0.00 0.00 30.59 4.94
4320 4551 3.125520 AACCCATGACCCACACAAC 57.874 52.632 0.00 0.00 0.00 3.32
4321 4552 0.469144 AACCCATGACCCACACAACC 60.469 55.000 0.00 0.00 0.00 3.77
4322 4553 1.152599 CCCATGACCCACACAACCA 59.847 57.895 0.00 0.00 0.00 3.67
4323 4554 1.178534 CCCATGACCCACACAACCAC 61.179 60.000 0.00 0.00 0.00 4.16
4324 4555 1.514678 CCATGACCCACACAACCACG 61.515 60.000 0.00 0.00 0.00 4.94
4325 4556 0.533978 CATGACCCACACAACCACGA 60.534 55.000 0.00 0.00 0.00 4.35
4326 4557 0.534203 ATGACCCACACAACCACGAC 60.534 55.000 0.00 0.00 0.00 4.34
4327 4558 1.890510 GACCCACACAACCACGACC 60.891 63.158 0.00 0.00 0.00 4.79
4328 4559 2.593436 CCCACACAACCACGACCC 60.593 66.667 0.00 0.00 0.00 4.46
4329 4560 2.190843 CCACACAACCACGACCCA 59.809 61.111 0.00 0.00 0.00 4.51
4330 4561 1.452289 CCACACAACCACGACCCAA 60.452 57.895 0.00 0.00 0.00 4.12
4331 4562 1.444119 CCACACAACCACGACCCAAG 61.444 60.000 0.00 0.00 0.00 3.61
4332 4563 1.153046 ACACAACCACGACCCAAGG 60.153 57.895 0.00 0.00 0.00 3.61
4333 4564 1.147376 CACAACCACGACCCAAGGA 59.853 57.895 0.00 0.00 0.00 3.36
4334 4565 0.250727 CACAACCACGACCCAAGGAT 60.251 55.000 0.00 0.00 0.00 3.24
4335 4566 0.250727 ACAACCACGACCCAAGGATG 60.251 55.000 0.00 0.00 0.00 3.51
4336 4567 1.303317 AACCACGACCCAAGGATGC 60.303 57.895 0.00 0.00 0.00 3.91
4337 4568 2.819595 CCACGACCCAAGGATGCG 60.820 66.667 0.00 0.00 0.00 4.73
4338 4569 2.047274 CACGACCCAAGGATGCGT 60.047 61.111 0.00 0.00 35.33 5.24
4339 4570 2.100631 CACGACCCAAGGATGCGTC 61.101 63.158 0.00 0.00 32.20 5.19
4340 4571 2.264480 CGACCCAAGGATGCGTCA 59.736 61.111 8.47 0.00 34.65 4.35
4341 4572 1.153369 CGACCCAAGGATGCGTCAT 60.153 57.895 8.47 0.00 34.65 3.06
4342 4573 1.154205 CGACCCAAGGATGCGTCATC 61.154 60.000 8.47 10.26 39.87 2.92
4343 4574 1.153369 ACCCAAGGATGCGTCATCG 60.153 57.895 8.47 0.00 41.35 3.84
4344 4575 1.153369 CCCAAGGATGCGTCATCGT 60.153 57.895 8.47 10.20 41.35 3.73
4345 4576 1.431488 CCCAAGGATGCGTCATCGTG 61.431 60.000 8.47 12.32 41.35 4.35
4346 4577 0.460109 CCAAGGATGCGTCATCGTGA 60.460 55.000 8.47 0.00 41.35 4.35
4347 4578 0.647410 CAAGGATGCGTCATCGTGAC 59.353 55.000 8.47 7.74 43.65 3.67
4348 4579 0.532573 AAGGATGCGTCATCGTGACT 59.467 50.000 8.47 4.14 44.85 3.41
4349 4580 0.179127 AGGATGCGTCATCGTGACTG 60.179 55.000 8.47 9.53 44.85 3.51
4350 4581 0.179137 GGATGCGTCATCGTGACTGA 60.179 55.000 8.47 3.70 44.85 3.41
4351 4582 1.536922 GGATGCGTCATCGTGACTGAT 60.537 52.381 8.47 7.22 44.85 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.945640 ACTTTGGTAGGAGTGGTTGTT 57.054 42.857 0.00 0.00 0.00 2.83
40 41 3.496331 CAGGACTGCCCTCCTTTTTAAA 58.504 45.455 0.00 0.00 45.60 1.52
43 44 0.113190 CCAGGACTGCCCTCCTTTTT 59.887 55.000 0.00 0.00 45.60 1.94
62 63 6.706716 ACTTGCTGACCTCTTTTCTAGTTAAC 59.293 38.462 0.00 0.00 0.00 2.01
103 104 3.005155 GCCCACCAATATCTTTCAGATGC 59.995 47.826 0.00 0.00 35.37 3.91
104 105 3.251729 CGCCCACCAATATCTTTCAGATG 59.748 47.826 0.00 0.00 35.37 2.90
105 106 3.480470 CGCCCACCAATATCTTTCAGAT 58.520 45.455 0.00 0.00 38.70 2.90
106 107 2.917933 CGCCCACCAATATCTTTCAGA 58.082 47.619 0.00 0.00 0.00 3.27
107 108 1.334869 GCGCCCACCAATATCTTTCAG 59.665 52.381 0.00 0.00 0.00 3.02
253 257 3.132467 ACTCCTACACGAAGGGAAATAGC 59.868 47.826 0.00 0.00 37.24 2.97
260 264 3.396260 TTTCAACTCCTACACGAAGGG 57.604 47.619 0.00 0.00 37.24 3.95
268 272 6.560253 ATGACATGTGTTTTCAACTCCTAC 57.440 37.500 1.15 0.00 0.00 3.18
319 323 3.186613 GTGGAGCAAGACCTTTAGAAACG 59.813 47.826 0.00 0.00 0.00 3.60
385 389 6.711194 TGTGGTTGTTCTTCGTTTTATATCCA 59.289 34.615 0.00 0.00 0.00 3.41
433 437 3.555956 GTCATGTCCATACGGATCAACAC 59.444 47.826 0.00 0.00 45.33 3.32
435 439 3.792401 TGTCATGTCCATACGGATCAAC 58.208 45.455 0.00 0.00 45.33 3.18
436 440 4.441792 CTTGTCATGTCCATACGGATCAA 58.558 43.478 0.00 0.00 45.33 2.57
437 441 3.741075 GCTTGTCATGTCCATACGGATCA 60.741 47.826 0.00 0.00 45.33 2.92
438 442 2.802816 GCTTGTCATGTCCATACGGATC 59.197 50.000 0.00 0.00 45.33 3.36
439 443 2.435805 AGCTTGTCATGTCCATACGGAT 59.564 45.455 0.00 0.00 45.33 4.18
440 444 1.831106 AGCTTGTCATGTCCATACGGA 59.169 47.619 0.00 0.00 39.79 4.69
441 445 2.205074 GAGCTTGTCATGTCCATACGG 58.795 52.381 0.00 0.00 0.00 4.02
442 446 2.862536 CTGAGCTTGTCATGTCCATACG 59.137 50.000 0.00 0.00 33.51 3.06
443 447 2.611292 GCTGAGCTTGTCATGTCCATAC 59.389 50.000 0.00 0.00 33.51 2.39
444 448 2.236893 TGCTGAGCTTGTCATGTCCATA 59.763 45.455 5.83 0.00 33.51 2.74
458 462 1.367599 GAGATGTGGTGCTGCTGAGC 61.368 60.000 0.00 0.00 46.44 4.26
464 468 3.519579 CTCTTGTAGAGATGTGGTGCTG 58.480 50.000 0.00 0.00 45.07 4.41
465 469 2.093764 GCTCTTGTAGAGATGTGGTGCT 60.094 50.000 7.85 0.00 45.07 4.40
472 476 3.472283 AGCCATGCTCTTGTAGAGATG 57.528 47.619 7.85 8.03 45.07 2.90
485 489 0.961019 TTCACTGTTTGGAGCCATGC 59.039 50.000 0.00 0.00 0.00 4.06
489 493 0.804989 CGGATTCACTGTTTGGAGCC 59.195 55.000 0.00 0.00 35.63 4.70
502 506 1.871080 ATGGTGCTTCGATCGGATTC 58.129 50.000 16.41 1.90 0.00 2.52
507 511 6.287107 AGTTTAATTATGGTGCTTCGATCG 57.713 37.500 9.36 9.36 0.00 3.69
518 522 8.635124 CACAACGCAAAACTAGTTTAATTATGG 58.365 33.333 20.83 11.09 31.63 2.74
542 546 7.298122 TCGAAATGATTGAAGCTAAGAAACAC 58.702 34.615 0.00 0.00 0.00 3.32
576 580 9.807921 TCTTTGGTTCTAAATTAGAATTGAGGT 57.192 29.630 17.26 0.00 45.63 3.85
587 591 8.793592 GTGGATTGTACTCTTTGGTTCTAAATT 58.206 33.333 0.00 0.00 0.00 1.82
588 592 7.119262 CGTGGATTGTACTCTTTGGTTCTAAAT 59.881 37.037 0.00 0.00 0.00 1.40
600 604 1.557099 TCCAGCGTGGATTGTACTCT 58.443 50.000 3.02 0.00 42.67 3.24
620 624 4.340950 TCATTTCTTTGACCTGTTCCAACC 59.659 41.667 0.00 0.00 0.00 3.77
648 652 1.971357 GAGAGGAAGAGTTGGTGGTCA 59.029 52.381 0.00 0.00 0.00 4.02
661 665 1.938585 ACGATTCTGGGTGAGAGGAA 58.061 50.000 0.00 0.00 30.18 3.36
696 700 2.266055 CAGTTCGCCTCTCACCCC 59.734 66.667 0.00 0.00 0.00 4.95
939 943 4.108299 TACGTACGGCGAGGGGGA 62.108 66.667 21.06 0.00 44.77 4.81
940 944 3.892581 GTACGTACGGCGAGGGGG 61.893 72.222 21.06 0.00 44.77 5.40
941 945 3.133464 TGTACGTACGGCGAGGGG 61.133 66.667 21.06 1.78 44.77 4.79
1007 1011 4.119940 CCAAAATTGCGCGCGTGC 62.120 61.111 35.99 35.99 37.91 5.34
1046 1050 2.637383 GCTCCCTGACGACGAGGTT 61.637 63.158 0.00 0.00 0.00 3.50
1217 1221 2.095252 GCTGAAGAAGGACGACGGC 61.095 63.158 0.00 0.00 0.00 5.68
1308 1312 1.312371 CGCCAACGGAATTCCATGGT 61.312 55.000 31.84 18.68 41.92 3.55
1357 1366 0.747852 ACCAACCAAAACCGCGAATT 59.252 45.000 8.23 0.00 0.00 2.17
1525 1534 4.443266 GCCTCCTCGCTGTTCGCT 62.443 66.667 0.00 0.00 38.27 4.93
1604 1619 3.027170 GACAGCGCATGGTTCGTGG 62.027 63.158 11.47 0.00 0.00 4.94
1618 1633 1.006102 ACAAAGTCGCCGAGGACAG 60.006 57.895 8.24 1.60 39.42 3.51
1654 1669 8.443160 TGAAGAAAAATCGTATTCTAGTGCAAG 58.557 33.333 0.00 0.00 34.90 4.01
1669 1684 3.119990 TGGACGCGGAATGAAGAAAAATC 60.120 43.478 12.47 0.00 0.00 2.17
1764 1779 3.056179 TCCGCTAATCAATCACTGTCACA 60.056 43.478 0.00 0.00 0.00 3.58
1769 1785 3.065371 GGGTTTCCGCTAATCAATCACTG 59.935 47.826 0.00 0.00 0.00 3.66
1799 1815 9.462606 AATTTAAAATTAGGGAATCTCTCGTGT 57.537 29.630 0.00 0.00 0.00 4.49
1853 1869 3.596066 CTGCTGGCCTGTGTACGCT 62.596 63.158 11.69 0.00 0.00 5.07
2419 2456 5.904941 TCGAAGTACAAGTTGAAGTTGGTA 58.095 37.500 16.33 4.77 32.93 3.25
2423 2460 8.674607 AGAAAAATCGAAGTACAAGTTGAAGTT 58.325 29.630 10.54 0.00 0.00 2.66
2425 2462 7.587757 CCAGAAAAATCGAAGTACAAGTTGAAG 59.412 37.037 10.54 0.00 0.00 3.02
2428 2465 6.954944 TCCAGAAAAATCGAAGTACAAGTTG 58.045 36.000 0.00 0.00 0.00 3.16
2429 2466 7.094762 GGATCCAGAAAAATCGAAGTACAAGTT 60.095 37.037 6.95 0.00 0.00 2.66
2434 2471 6.543736 GTTGGATCCAGAAAAATCGAAGTAC 58.456 40.000 15.53 0.92 0.00 2.73
2435 2472 5.350365 CGTTGGATCCAGAAAAATCGAAGTA 59.650 40.000 15.53 0.00 0.00 2.24
2437 2474 4.154195 ACGTTGGATCCAGAAAAATCGAAG 59.846 41.667 15.53 1.62 0.00 3.79
2439 2476 3.435327 CACGTTGGATCCAGAAAAATCGA 59.565 43.478 15.53 0.00 0.00 3.59
2440 2477 3.188460 ACACGTTGGATCCAGAAAAATCG 59.812 43.478 15.53 13.49 0.00 3.34
2441 2478 4.766404 ACACGTTGGATCCAGAAAAATC 57.234 40.909 15.53 0.67 0.00 2.17
2442 2479 7.556275 ACATATACACGTTGGATCCAGAAAAAT 59.444 33.333 15.53 8.41 0.00 1.82
2447 2484 5.278120 CGTACATATACACGTTGGATCCAGA 60.278 44.000 15.53 3.48 33.56 3.86
2448 2485 4.915667 CGTACATATACACGTTGGATCCAG 59.084 45.833 15.53 7.02 33.56 3.86
2449 2486 4.579753 TCGTACATATACACGTTGGATCCA 59.420 41.667 11.44 11.44 39.18 3.41
2450 2487 5.112220 TCGTACATATACACGTTGGATCC 57.888 43.478 4.20 4.20 39.18 3.36
2451 2488 5.755813 ACTCGTACATATACACGTTGGATC 58.244 41.667 7.81 0.00 39.18 3.36
2452 2489 5.762825 ACTCGTACATATACACGTTGGAT 57.237 39.130 7.81 0.00 39.18 3.41
2453 2490 5.334319 CAACTCGTACATATACACGTTGGA 58.666 41.667 7.81 0.00 37.41 3.53
2454 2491 4.027132 GCAACTCGTACATATACACGTTGG 60.027 45.833 11.96 3.94 39.32 3.77
2455 2492 4.559643 TGCAACTCGTACATATACACGTTG 59.440 41.667 7.72 7.72 40.54 4.10
2456 2493 4.735985 TGCAACTCGTACATATACACGTT 58.264 39.130 7.81 0.00 39.18 3.99
2457 2494 4.359971 TGCAACTCGTACATATACACGT 57.640 40.909 7.81 0.00 39.18 4.49
2458 2495 5.231357 ACAATGCAACTCGTACATATACACG 59.769 40.000 0.00 2.63 39.48 4.49
2459 2496 6.583912 ACAATGCAACTCGTACATATACAC 57.416 37.500 0.00 0.00 0.00 2.90
2463 2500 5.182487 TCCAACAATGCAACTCGTACATAT 58.818 37.500 0.00 0.00 0.00 1.78
2481 2518 5.183331 GGTTAATTTCCTCTGTTCCTCCAAC 59.817 44.000 0.00 0.00 35.28 3.77
2511 2548 0.532115 CCTCCTGAAAATTTGGCCGG 59.468 55.000 0.00 0.00 0.00 6.13
2557 2594 3.679738 CGGTTGCCGGCCATGTTT 61.680 61.111 26.77 0.00 44.15 2.83
2933 3075 4.619227 CTGTGTCCCGGCCACGTT 62.619 66.667 15.21 0.00 38.78 3.99
2991 3142 4.735132 TGAAGCCGAACGAGCCCG 62.735 66.667 0.00 0.00 42.50 6.13
3037 3188 2.535788 CGCCGTCGGGTTGTCAAAA 61.536 57.895 14.38 0.00 34.97 2.44
3040 3191 4.651008 GACGCCGTCGGGTTGTCA 62.651 66.667 14.38 0.00 39.31 3.58
3077 3228 2.099431 CGTTCTGCCTCTGCTGCTC 61.099 63.158 0.00 0.00 38.71 4.26
3109 3260 2.759973 TCCTCCTTGGCGCTCGAT 60.760 61.111 7.64 0.00 35.26 3.59
3175 3326 2.886523 TCCTTTGCCATTTCTGACACTG 59.113 45.455 0.00 0.00 0.00 3.66
3194 3345 1.226717 GCTCCATCTCGTCGTGTCC 60.227 63.158 0.00 0.00 0.00 4.02
3224 3375 9.780413 GCCTATCCTAGTACAATTACGTATTAC 57.220 37.037 0.00 0.00 32.93 1.89
3294 3447 1.007387 GAACCCTTTTGTGCAGCCG 60.007 57.895 0.00 0.00 0.00 5.52
3310 3464 3.132925 CCGTCGTGTTAAAAGAAGGGAA 58.867 45.455 0.00 0.00 33.42 3.97
3318 3472 6.900568 TTTCTTTACTCCGTCGTGTTAAAA 57.099 33.333 0.00 0.00 0.00 1.52
3321 3475 8.761575 AATATTTTCTTTACTCCGTCGTGTTA 57.238 30.769 0.00 0.00 0.00 2.41
3399 3553 3.013921 TCTGTGTGGAAGTGGAAACAAC 58.986 45.455 0.00 0.00 46.06 3.32
3511 3666 9.944376 ACTAGTTCAGTGATTTAAATGCTCTTA 57.056 29.630 5.17 0.00 35.62 2.10
3512 3667 8.854614 ACTAGTTCAGTGATTTAAATGCTCTT 57.145 30.769 5.17 0.00 35.62 2.85
3513 3668 9.944376 TTACTAGTTCAGTGATTTAAATGCTCT 57.056 29.630 5.17 1.65 38.24 4.09
3524 3679 9.757227 GAGCATTTAGATTACTAGTTCAGTGAT 57.243 33.333 0.00 0.00 38.24 3.06
3525 3680 8.972127 AGAGCATTTAGATTACTAGTTCAGTGA 58.028 33.333 0.00 0.00 38.24 3.41
3526 3681 9.593134 AAGAGCATTTAGATTACTAGTTCAGTG 57.407 33.333 0.00 0.00 38.24 3.66
3563 3718 9.268282 ACCACTATCTAATAATCCATCCGTAAT 57.732 33.333 0.00 0.00 0.00 1.89
3564 3719 8.660295 ACCACTATCTAATAATCCATCCGTAA 57.340 34.615 0.00 0.00 0.00 3.18
3565 3720 9.931698 ATACCACTATCTAATAATCCATCCGTA 57.068 33.333 0.00 0.00 0.00 4.02
3566 3721 8.696374 CATACCACTATCTAATAATCCATCCGT 58.304 37.037 0.00 0.00 0.00 4.69
3567 3722 8.696374 ACATACCACTATCTAATAATCCATCCG 58.304 37.037 0.00 0.00 0.00 4.18
3605 3803 6.402222 ACATCTGAGGTCTGATACACTTTTC 58.598 40.000 0.00 0.00 33.94 2.29
3606 3804 6.365970 ACATCTGAGGTCTGATACACTTTT 57.634 37.500 0.00 0.00 33.94 2.27
3608 3806 6.191315 AGTACATCTGAGGTCTGATACACTT 58.809 40.000 0.00 0.00 33.94 3.16
3615 3813 4.013050 CAGTGAGTACATCTGAGGTCTGA 58.987 47.826 0.00 0.00 31.71 3.27
3645 3851 5.468746 TCAGTCTGTACAAGTACAAAATGGC 59.531 40.000 12.43 4.62 44.47 4.40
3646 3852 7.011950 TGTTCAGTCTGTACAAGTACAAAATGG 59.988 37.037 12.43 3.19 44.47 3.16
3656 3862 4.508124 GTCTGGTTGTTCAGTCTGTACAAG 59.492 45.833 21.33 12.50 38.11 3.16
3790 4004 4.134563 CCTAAATGGATGGTTAGTTCGGG 58.865 47.826 0.00 0.00 38.35 5.14
3813 4027 3.552594 CCGGGGAGGGAGAGAAATA 57.447 57.895 0.00 0.00 35.97 1.40
3831 4062 3.135994 TCGCTTTAGTCAGTGAAAACCC 58.864 45.455 0.00 0.00 30.13 4.11
3837 4068 4.451096 GGTCAAAATCGCTTTAGTCAGTGA 59.549 41.667 0.00 0.00 37.69 3.41
3838 4069 4.213270 TGGTCAAAATCGCTTTAGTCAGTG 59.787 41.667 0.00 0.00 0.00 3.66
3841 4072 4.155826 CCATGGTCAAAATCGCTTTAGTCA 59.844 41.667 2.57 0.00 0.00 3.41
3846 4077 2.890311 TCACCATGGTCAAAATCGCTTT 59.110 40.909 16.53 0.00 0.00 3.51
3847 4078 2.228822 GTCACCATGGTCAAAATCGCTT 59.771 45.455 16.53 0.00 0.00 4.68
3849 4080 1.812571 AGTCACCATGGTCAAAATCGC 59.187 47.619 16.53 0.00 0.00 4.58
3861 4092 1.614317 GGCTAACTTGGCAGTCACCAT 60.614 52.381 0.00 0.00 40.13 3.55
3873 4104 2.440247 GGCATGGCGGGCTAACTT 60.440 61.111 2.41 0.00 0.00 2.66
3887 4118 3.153919 GTCCCACATTAAAGAGTTGGCA 58.846 45.455 0.00 0.00 0.00 4.92
3892 4123 2.290960 GCTGGGTCCCACATTAAAGAGT 60.291 50.000 6.47 0.00 0.00 3.24
3896 4127 3.692690 GTTAGCTGGGTCCCACATTAAA 58.307 45.455 6.47 0.00 0.00 1.52
3906 4137 2.135933 GATATGTGCGTTAGCTGGGTC 58.864 52.381 0.00 0.00 45.42 4.46
3910 4141 2.929398 TGTGTGATATGTGCGTTAGCTG 59.071 45.455 0.00 0.00 45.42 4.24
3911 4142 2.930040 GTGTGTGATATGTGCGTTAGCT 59.070 45.455 0.00 0.00 45.42 3.32
3912 4143 2.030457 GGTGTGTGATATGTGCGTTAGC 59.970 50.000 0.00 0.00 45.41 3.09
3913 4144 3.521560 AGGTGTGTGATATGTGCGTTAG 58.478 45.455 0.00 0.00 0.00 2.34
3914 4145 3.517602 GAGGTGTGTGATATGTGCGTTA 58.482 45.455 0.00 0.00 0.00 3.18
3915 4146 2.346803 GAGGTGTGTGATATGTGCGTT 58.653 47.619 0.00 0.00 0.00 4.84
3916 4147 1.405526 GGAGGTGTGTGATATGTGCGT 60.406 52.381 0.00 0.00 0.00 5.24
3917 4148 1.290203 GGAGGTGTGTGATATGTGCG 58.710 55.000 0.00 0.00 0.00 5.34
3918 4149 2.009774 GTGGAGGTGTGTGATATGTGC 58.990 52.381 0.00 0.00 0.00 4.57
3923 4154 0.902984 AGCGGTGGAGGTGTGTGATA 60.903 55.000 0.00 0.00 0.00 2.15
3928 4159 1.071471 AAGAAGCGGTGGAGGTGTG 59.929 57.895 0.00 0.00 0.00 3.82
3957 4188 0.393077 AGGAGTGGTTCTCGTGGTTG 59.607 55.000 0.00 0.00 43.60 3.77
3958 4189 0.680061 GAGGAGTGGTTCTCGTGGTT 59.320 55.000 0.00 0.00 43.60 3.67
3959 4190 1.186267 GGAGGAGTGGTTCTCGTGGT 61.186 60.000 0.00 0.00 43.60 4.16
3960 4191 1.592223 GGAGGAGTGGTTCTCGTGG 59.408 63.158 0.00 0.00 43.60 4.94
3961 4192 1.185618 TGGGAGGAGTGGTTCTCGTG 61.186 60.000 0.00 0.00 43.60 4.35
3962 4193 1.155390 TGGGAGGAGTGGTTCTCGT 59.845 57.895 0.00 0.00 43.60 4.18
3963 4194 0.900647 AGTGGGAGGAGTGGTTCTCG 60.901 60.000 0.00 0.00 43.60 4.04
3964 4195 1.276705 GAAGTGGGAGGAGTGGTTCTC 59.723 57.143 0.00 0.00 42.07 2.87
3965 4196 1.353091 GAAGTGGGAGGAGTGGTTCT 58.647 55.000 0.00 0.00 0.00 3.01
3966 4197 0.037232 CGAAGTGGGAGGAGTGGTTC 60.037 60.000 0.00 0.00 0.00 3.62
3967 4198 0.763223 ACGAAGTGGGAGGAGTGGTT 60.763 55.000 0.00 0.00 42.51 3.67
3968 4199 1.152312 ACGAAGTGGGAGGAGTGGT 60.152 57.895 0.00 0.00 42.51 4.16
3969 4200 3.793060 ACGAAGTGGGAGGAGTGG 58.207 61.111 0.00 0.00 42.51 4.00
3981 4212 1.170290 GGGTTTGGGTGGTGACGAAG 61.170 60.000 0.00 0.00 0.00 3.79
3982 4213 1.152922 GGGTTTGGGTGGTGACGAA 60.153 57.895 0.00 0.00 0.00 3.85
3983 4214 2.511900 GGGTTTGGGTGGTGACGA 59.488 61.111 0.00 0.00 0.00 4.20
3984 4215 2.596338 GGGGTTTGGGTGGTGACG 60.596 66.667 0.00 0.00 0.00 4.35
3985 4216 1.830847 GTGGGGTTTGGGTGGTGAC 60.831 63.158 0.00 0.00 0.00 3.67
3986 4217 2.604152 GTGGGGTTTGGGTGGTGA 59.396 61.111 0.00 0.00 0.00 4.02
3987 4218 2.523168 GGTGGGGTTTGGGTGGTG 60.523 66.667 0.00 0.00 0.00 4.17
3988 4219 2.306715 GAAGGTGGGGTTTGGGTGGT 62.307 60.000 0.00 0.00 0.00 4.16
3989 4220 1.533033 GAAGGTGGGGTTTGGGTGG 60.533 63.158 0.00 0.00 0.00 4.61
3990 4221 1.533033 GGAAGGTGGGGTTTGGGTG 60.533 63.158 0.00 0.00 0.00 4.61
3991 4222 2.785776 GGGAAGGTGGGGTTTGGGT 61.786 63.158 0.00 0.00 0.00 4.51
3992 4223 2.119611 GGGAAGGTGGGGTTTGGG 59.880 66.667 0.00 0.00 0.00 4.12
3993 4224 1.118965 GTTGGGAAGGTGGGGTTTGG 61.119 60.000 0.00 0.00 0.00 3.28
3994 4225 1.118965 GGTTGGGAAGGTGGGGTTTG 61.119 60.000 0.00 0.00 0.00 2.93
3995 4226 1.234820 GGTTGGGAAGGTGGGGTTT 59.765 57.895 0.00 0.00 0.00 3.27
3996 4227 2.015726 TGGTTGGGAAGGTGGGGTT 61.016 57.895 0.00 0.00 0.00 4.11
3997 4228 2.370403 TGGTTGGGAAGGTGGGGT 60.370 61.111 0.00 0.00 0.00 4.95
3998 4229 2.117423 GTGGTTGGGAAGGTGGGG 59.883 66.667 0.00 0.00 0.00 4.96
3999 4230 2.117423 GGTGGTTGGGAAGGTGGG 59.883 66.667 0.00 0.00 0.00 4.61
4000 4231 1.228552 CAGGTGGTTGGGAAGGTGG 60.229 63.158 0.00 0.00 0.00 4.61
4001 4232 0.250901 CTCAGGTGGTTGGGAAGGTG 60.251 60.000 0.00 0.00 0.00 4.00
4002 4233 0.697854 ACTCAGGTGGTTGGGAAGGT 60.698 55.000 0.00 0.00 0.00 3.50
4003 4234 0.478507 AACTCAGGTGGTTGGGAAGG 59.521 55.000 0.00 0.00 0.00 3.46
4004 4235 1.142870 TCAACTCAGGTGGTTGGGAAG 59.857 52.381 0.00 0.00 42.76 3.46
4005 4236 1.217916 TCAACTCAGGTGGTTGGGAA 58.782 50.000 0.00 0.00 42.76 3.97
4006 4237 1.073763 CATCAACTCAGGTGGTTGGGA 59.926 52.381 0.00 0.00 42.76 4.37
4007 4238 1.202927 ACATCAACTCAGGTGGTTGGG 60.203 52.381 0.00 3.26 42.76 4.12
4008 4239 2.154462 GACATCAACTCAGGTGGTTGG 58.846 52.381 0.00 0.00 42.76 3.77
4009 4240 1.800586 CGACATCAACTCAGGTGGTTG 59.199 52.381 0.00 0.00 43.57 3.77
4010 4241 1.878102 GCGACATCAACTCAGGTGGTT 60.878 52.381 0.00 0.00 0.00 3.67
4011 4242 0.320771 GCGACATCAACTCAGGTGGT 60.321 55.000 0.00 0.00 0.00 4.16
4012 4243 0.320683 TGCGACATCAACTCAGGTGG 60.321 55.000 0.00 0.00 0.00 4.61
4013 4244 0.792640 GTGCGACATCAACTCAGGTG 59.207 55.000 0.00 0.00 0.00 4.00
4014 4245 0.392706 TGTGCGACATCAACTCAGGT 59.607 50.000 0.00 0.00 0.00 4.00
4015 4246 1.395954 CATGTGCGACATCAACTCAGG 59.604 52.381 0.00 0.00 36.53 3.86
4016 4247 2.071540 ACATGTGCGACATCAACTCAG 58.928 47.619 0.00 0.00 36.53 3.35
4017 4248 1.799994 CACATGTGCGACATCAACTCA 59.200 47.619 13.94 0.00 36.53 3.41
4018 4249 2.515641 CACATGTGCGACATCAACTC 57.484 50.000 13.94 0.00 36.53 3.01
4030 4261 2.747460 CGGTCCAGGGCACATGTG 60.747 66.667 21.83 21.83 0.00 3.21
4031 4262 2.829384 AACGGTCCAGGGCACATGT 61.829 57.895 0.00 0.00 0.00 3.21
4032 4263 2.034066 AACGGTCCAGGGCACATG 59.966 61.111 0.00 0.00 0.00 3.21
4033 4264 2.034066 CAACGGTCCAGGGCACAT 59.966 61.111 0.00 0.00 0.00 3.21
4034 4265 3.484806 ACAACGGTCCAGGGCACA 61.485 61.111 0.00 0.00 0.00 4.57
4035 4266 2.978010 CACAACGGTCCAGGGCAC 60.978 66.667 0.00 0.00 0.00 5.01
4036 4267 4.947147 GCACAACGGTCCAGGGCA 62.947 66.667 0.00 0.00 0.00 5.36
4039 4270 4.619227 ACGGCACAACGGTCCAGG 62.619 66.667 0.00 0.00 38.39 4.45
4040 4271 3.345808 CACGGCACAACGGTCCAG 61.346 66.667 0.00 0.00 38.39 3.86
4302 4533 0.469144 GGTTGTGTGGGTCATGGGTT 60.469 55.000 0.00 0.00 0.00 4.11
4303 4534 1.152830 GGTTGTGTGGGTCATGGGT 59.847 57.895 0.00 0.00 0.00 4.51
4304 4535 1.152599 TGGTTGTGTGGGTCATGGG 59.847 57.895 0.00 0.00 0.00 4.00
4305 4536 1.514678 CGTGGTTGTGTGGGTCATGG 61.515 60.000 0.00 0.00 0.00 3.66
4306 4537 0.533978 TCGTGGTTGTGTGGGTCATG 60.534 55.000 0.00 0.00 0.00 3.07
4307 4538 0.534203 GTCGTGGTTGTGTGGGTCAT 60.534 55.000 0.00 0.00 0.00 3.06
4308 4539 1.153329 GTCGTGGTTGTGTGGGTCA 60.153 57.895 0.00 0.00 0.00 4.02
4309 4540 1.890510 GGTCGTGGTTGTGTGGGTC 60.891 63.158 0.00 0.00 0.00 4.46
4310 4541 2.191109 GGTCGTGGTTGTGTGGGT 59.809 61.111 0.00 0.00 0.00 4.51
4311 4542 2.593436 GGGTCGTGGTTGTGTGGG 60.593 66.667 0.00 0.00 0.00 4.61
4312 4543 1.444119 CTTGGGTCGTGGTTGTGTGG 61.444 60.000 0.00 0.00 0.00 4.17
4313 4544 1.444119 CCTTGGGTCGTGGTTGTGTG 61.444 60.000 0.00 0.00 0.00 3.82
4314 4545 1.153046 CCTTGGGTCGTGGTTGTGT 60.153 57.895 0.00 0.00 0.00 3.72
4315 4546 0.250727 ATCCTTGGGTCGTGGTTGTG 60.251 55.000 0.00 0.00 0.00 3.33
4316 4547 0.250727 CATCCTTGGGTCGTGGTTGT 60.251 55.000 0.00 0.00 0.00 3.32
4317 4548 1.586154 GCATCCTTGGGTCGTGGTTG 61.586 60.000 0.00 0.00 0.00 3.77
4318 4549 1.303317 GCATCCTTGGGTCGTGGTT 60.303 57.895 0.00 0.00 0.00 3.67
4319 4550 2.351276 GCATCCTTGGGTCGTGGT 59.649 61.111 0.00 0.00 0.00 4.16
4320 4551 2.819595 CGCATCCTTGGGTCGTGG 60.820 66.667 0.00 0.00 0.00 4.94
4321 4552 2.047274 ACGCATCCTTGGGTCGTG 60.047 61.111 0.00 0.00 45.01 4.35
4326 4557 1.153369 ACGATGACGCATCCTTGGG 60.153 57.895 12.27 3.43 43.96 4.12
4327 4558 0.460109 TCACGATGACGCATCCTTGG 60.460 55.000 12.27 3.70 43.96 3.61
4328 4559 0.647410 GTCACGATGACGCATCCTTG 59.353 55.000 12.27 10.22 43.96 3.61
4329 4560 3.050703 GTCACGATGACGCATCCTT 57.949 52.632 12.27 0.47 43.96 3.36
4330 4561 4.814900 GTCACGATGACGCATCCT 57.185 55.556 12.27 1.40 43.96 3.24


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

AutoCloner maintained by Alex Coulton.