Multiple sequence alignment - TraesCS4A01G040600

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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 TraesCS4A01G040600 chr4A 100.000 3224 0 0 1 3224 34028976 34025753 0.000000e+00 5954.0
1 TraesCS4A01G040600 chr4A 82.237 152 19 5 1 146 710747207 710747356 1.210000e-24 124.0
2 TraesCS4A01G040600 chr4D 89.552 2412 169 39 154 2532 432750664 432748303 0.000000e+00 2981.0
3 TraesCS4A01G040600 chr4D 91.803 366 22 3 2855 3220 432747684 432747327 1.340000e-138 503.0
4 TraesCS4A01G040600 chr4D 89.655 145 13 2 2537 2681 432747821 432747679 1.980000e-42 183.0
5 TraesCS4A01G040600 chr4B 88.232 1725 94 59 709 2361 530519360 530521047 0.000000e+00 1960.0
6 TraesCS4A01G040600 chr4B 89.751 361 20 9 2869 3218 530521453 530521807 2.280000e-121 446.0
7 TraesCS4A01G040600 chr4B 95.745 47 2 0 2361 2407 530521071 530521117 3.450000e-10 76.8
8 TraesCS4A01G040600 chr7D 83.309 689 95 11 1 669 621745183 621744495 4.570000e-173 617.0
9 TraesCS4A01G040600 chr7D 80.088 683 106 15 2 660 45122862 45122186 6.260000e-132 481.0
10 TraesCS4A01G040600 chr3D 82.828 693 98 13 3 682 573266292 573266976 4.600000e-168 601.0
11 TraesCS4A01G040600 chr3D 87.952 83 7 2 2773 2854 589426879 589426959 9.520000e-16 95.3
12 TraesCS4A01G040600 chr3A 81.241 661 97 12 14 661 707925963 707926609 2.870000e-140 508.0
13 TraesCS4A01G040600 chr3B 83.154 558 85 5 154 702 11085760 11086317 4.800000e-138 501.0
14 TraesCS4A01G040600 chr1A 82.609 575 88 8 128 696 369493539 369492971 6.210000e-137 497.0
15 TraesCS4A01G040600 chr1D 80.147 680 89 17 1 669 491744919 491744275 1.750000e-127 466.0
16 TraesCS4A01G040600 chr2A 78.708 681 102 17 3 658 552643245 552642583 6.440000e-112 414.0
17 TraesCS4A01G040600 chr2B 85.268 224 29 2 451 670 92596789 92596566 9.000000e-56 228.0
18 TraesCS4A01G040600 chr2B 80.156 257 42 8 1478 1730 573975110 573975361 1.980000e-42 183.0
19 TraesCS4A01G040600 chr2B 82.482 137 19 5 1596 1730 573985068 573985201 7.310000e-22 115.0
20 TraesCS4A01G040600 chr5A 83.133 249 38 3 1 245 601241750 601241998 1.160000e-54 224.0
21 TraesCS4A01G040600 chr5A 84.466 103 13 3 2751 2852 331395635 331395735 7.360000e-17 99.0
22 TraesCS4A01G040600 chr2D 81.712 257 38 8 1478 1730 490118021 490118272 4.220000e-49 206.0
23 TraesCS4A01G040600 chr6D 82.099 162 23 5 527 682 18099765 18099604 2.020000e-27 134.0
24 TraesCS4A01G040600 chr6D 86.585 82 8 2 2774 2854 463646164 463646085 1.590000e-13 87.9
25 TraesCS4A01G040600 chr5D 81.081 148 19 6 519 659 40675523 40675668 3.400000e-20 110.0
26 TraesCS4A01G040600 chr5D 83.065 124 17 4 2732 2854 98737781 98737901 3.400000e-20 110.0
27 TraesCS4A01G040600 chr5D 87.273 55 6 1 2734 2788 39102288 39102341 9.660000e-06 62.1
28 TraesCS4A01G040600 chr6B 82.927 82 11 3 2774 2854 707000191 707000112 1.600000e-08 71.3


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 TraesCS4A01G040600 chr4A 34025753 34028976 3223 True 5954.000000 5954 100.000000 1 3224 1 chr4A.!!$R1 3223
1 TraesCS4A01G040600 chr4D 432747327 432750664 3337 True 1222.333333 2981 90.336667 154 3220 3 chr4D.!!$R1 3066
2 TraesCS4A01G040600 chr4B 530519360 530521807 2447 False 827.600000 1960 91.242667 709 3218 3 chr4B.!!$F1 2509
3 TraesCS4A01G040600 chr7D 621744495 621745183 688 True 617.000000 617 83.309000 1 669 1 chr7D.!!$R2 668
4 TraesCS4A01G040600 chr7D 45122186 45122862 676 True 481.000000 481 80.088000 2 660 1 chr7D.!!$R1 658
5 TraesCS4A01G040600 chr3D 573266292 573266976 684 False 601.000000 601 82.828000 3 682 1 chr3D.!!$F1 679
6 TraesCS4A01G040600 chr3A 707925963 707926609 646 False 508.000000 508 81.241000 14 661 1 chr3A.!!$F1 647
7 TraesCS4A01G040600 chr3B 11085760 11086317 557 False 501.000000 501 83.154000 154 702 1 chr3B.!!$F1 548
8 TraesCS4A01G040600 chr1A 369492971 369493539 568 True 497.000000 497 82.609000 128 696 1 chr1A.!!$R1 568
9 TraesCS4A01G040600 chr1D 491744275 491744919 644 True 466.000000 466 80.147000 1 669 1 chr1D.!!$R1 668
10 TraesCS4A01G040600 chr2A 552642583 552643245 662 True 414.000000 414 78.708000 3 658 1 chr2A.!!$R1 655

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
577 655 0.454285 GCGCGCTGAATTTTACTGCA 60.454 50.0 26.67 0.0 33.57 4.41 F
1275 1405 0.242017 CGGTCGTCTCCGGTAAGTTT 59.758 55.0 0.00 0.0 45.88 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2348 0.178990 AGCACTGTTCTTTCACCCCC 60.179 55.0 0.00 0.0 0.00 5.40 R
2724 3513 0.036732 CAAGACCCAGCTGGCTGTAA 59.963 55.0 28.39 0.0 42.15 2.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 0.734889 CGGCCGCAGATGAATTTCTT 59.265 50.000 14.67 0.00 0.00 2.52
81 83 2.066262 GAATTTCTTCGAGTGCGGACA 58.934 47.619 10.52 0.00 38.28 4.02
147 152 2.203070 GATCGCCGCCTCCAACAT 60.203 61.111 0.00 0.00 0.00 2.71
186 191 3.066190 ATCGCCGAGGTGGACGAA 61.066 61.111 2.57 0.00 45.05 3.85
250 255 1.472878 CCGTCGAGAATGAGTTCTGGA 59.527 52.381 0.00 0.00 44.57 3.86
302 310 2.742372 GGACAAGTGTGCGCGGAT 60.742 61.111 8.83 0.00 0.00 4.18
345 353 0.963856 ACCTAGGACATGCGTCGACA 60.964 55.000 17.98 0.00 43.61 4.35
369 378 1.676529 GACGATGAAGATCCTCGGTGA 59.323 52.381 9.28 0.00 38.54 4.02
386 397 2.671396 GGTGACTCGATGCATTTACGTT 59.329 45.455 0.00 0.00 0.00 3.99
434 460 4.361420 GGGAAGTAGTCTAGCATCGTTTC 58.639 47.826 0.00 0.00 0.00 2.78
440 466 7.197071 AGTAGTCTAGCATCGTTTCATCTAG 57.803 40.000 0.00 0.00 0.00 2.43
495 521 5.130350 GTTTGGGGCTTGAACTATGCTATA 58.870 41.667 0.00 0.00 0.00 1.31
526 576 6.476243 ACTGTAAATGTTTCCGTATGTGTC 57.524 37.500 0.00 0.00 0.00 3.67
574 652 1.226018 GCGCGCGCTGAATTTTACT 60.226 52.632 44.38 0.00 38.26 2.24
577 655 0.454285 GCGCGCTGAATTTTACTGCA 60.454 50.000 26.67 0.00 33.57 4.41
630 708 2.018324 GCAGCGCCTGAAAAAGCAC 61.018 57.895 2.29 0.00 32.44 4.40
631 709 1.656441 CAGCGCCTGAAAAAGCACT 59.344 52.632 2.29 0.00 32.44 4.40
639 717 2.417933 CCTGAAAAAGCACTCATCCTCG 59.582 50.000 0.00 0.00 0.00 4.63
644 726 2.125912 GCACTCATCCTCGTGCGT 60.126 61.111 0.00 0.00 45.74 5.24
651 733 2.070783 TCATCCTCGTGCGTTAAAACC 58.929 47.619 0.00 0.00 0.00 3.27
664 746 4.594136 CGTTAAAACCCTATTTCGATGCC 58.406 43.478 0.00 0.00 0.00 4.40
696 782 1.709578 AGCGCCTCTATTGGAGATGA 58.290 50.000 2.29 0.00 44.45 2.92
707 793 5.985530 TCTATTGGAGATGATTTACAGTGCG 59.014 40.000 0.00 0.00 0.00 5.34
735 821 2.344950 CATGTCACTCAAGCTCACTCC 58.655 52.381 0.00 0.00 0.00 3.85
751 840 0.459759 CTCCCTCGGTCGCTTTTACC 60.460 60.000 0.00 0.00 0.00 2.85
778 867 5.067805 GCTCCCGTTTCATTTTCCATTATCT 59.932 40.000 0.00 0.00 0.00 1.98
802 913 5.386958 AAACTAGCACACGATTACTCTGA 57.613 39.130 0.00 0.00 0.00 3.27
803 914 5.584253 AACTAGCACACGATTACTCTGAT 57.416 39.130 0.00 0.00 0.00 2.90
804 915 5.584253 ACTAGCACACGATTACTCTGATT 57.416 39.130 0.00 0.00 0.00 2.57
824 935 5.184287 TGATTATCGATCACTATTACCGGCA 59.816 40.000 0.00 0.00 39.83 5.69
833 944 3.990469 CACTATTACCGGCAGATGATGAC 59.010 47.826 0.00 0.00 0.00 3.06
838 949 1.233019 CCGGCAGATGATGACCAATC 58.767 55.000 0.00 0.00 30.50 2.67
868 979 2.099062 CACGCAGCATCGCTTTCC 59.901 61.111 0.00 0.00 36.40 3.13
932 1046 1.558233 ACCACTCCTAGTGCCAGTAC 58.442 55.000 1.43 0.00 44.63 2.73
935 1049 2.688958 CCACTCCTAGTGCCAGTACTAC 59.311 54.545 0.00 0.00 44.63 2.73
936 1050 2.355132 CACTCCTAGTGCCAGTACTACG 59.645 54.545 0.00 0.00 39.62 3.51
1061 1190 1.681264 CGCCCCTCAAAATATCCCAAC 59.319 52.381 0.00 0.00 0.00 3.77
1101 1231 5.641709 TCGATCAGAGCCGATCAAATATAC 58.358 41.667 8.57 0.00 41.65 1.47
1128 1258 1.480789 TGTTGATCGGGCACTAGCTA 58.519 50.000 0.00 0.00 41.70 3.32
1129 1259 1.409064 TGTTGATCGGGCACTAGCTAG 59.591 52.381 19.44 19.44 41.70 3.42
1183 1313 3.693807 TGATTTGCTGGAAAGATGAGCT 58.306 40.909 0.01 0.00 33.66 4.09
1275 1405 0.242017 CGGTCGTCTCCGGTAAGTTT 59.758 55.000 0.00 0.00 45.88 2.66
1278 1408 3.428045 CGGTCGTCTCCGGTAAGTTTAAT 60.428 47.826 0.00 0.00 45.88 1.40
1279 1409 4.108336 GGTCGTCTCCGGTAAGTTTAATC 58.892 47.826 0.00 0.00 33.95 1.75
1321 1451 1.081892 CTAGCGCACCATCCATATGC 58.918 55.000 11.47 0.00 35.96 3.14
1327 1465 2.217750 GCACCATCCATATGCACGTAA 58.782 47.619 0.00 0.00 39.23 3.18
1355 1501 2.442212 TCGAGTGTTCAACCGCAATA 57.558 45.000 0.00 0.00 0.00 1.90
1378 1524 2.810274 GCTGTTGCTGATTCTCAAGTGA 59.190 45.455 0.00 0.00 36.03 3.41
1389 1538 0.524862 CTCAAGTGAATGGTGCAGGC 59.475 55.000 0.00 0.00 0.00 4.85
1455 1604 2.433838 CAGGCAGCGAGTGGTGAG 60.434 66.667 0.00 0.00 46.53 3.51
1482 1634 3.533691 GACGACGCGGCGAAGAAG 61.534 66.667 44.35 11.91 34.83 2.85
1523 1675 0.391661 GCGCAGTTCCTGGAGATGAA 60.392 55.000 0.30 0.00 31.21 2.57
1536 1688 3.517100 TGGAGATGAACTTCAGGAAGGAG 59.483 47.826 13.19 0.00 42.53 3.69
1539 1691 0.321671 TGAACTTCAGGAAGGAGCGG 59.678 55.000 13.19 0.00 42.53 5.52
1542 1694 0.610687 ACTTCAGGAAGGAGCGGAAG 59.389 55.000 13.19 0.00 42.53 3.46
1729 1881 3.138798 TCGAGGCCGAGGTACAGC 61.139 66.667 0.00 0.00 40.30 4.40
1816 1981 6.852853 CACTTCACACACATAAATGACAGAAC 59.147 38.462 0.00 0.00 0.00 3.01
1827 1992 5.568620 AAATGACAGAACTCTTGGGTACT 57.431 39.130 0.00 0.00 0.00 2.73
1828 1993 6.681729 AAATGACAGAACTCTTGGGTACTA 57.318 37.500 0.00 0.00 0.00 1.82
1829 1994 6.875972 AATGACAGAACTCTTGGGTACTAT 57.124 37.500 0.00 0.00 0.00 2.12
1830 1995 7.973048 AATGACAGAACTCTTGGGTACTATA 57.027 36.000 0.00 0.00 0.00 1.31
1831 1996 6.770746 TGACAGAACTCTTGGGTACTATAC 57.229 41.667 0.00 0.00 0.00 1.47
1832 1997 5.356190 TGACAGAACTCTTGGGTACTATACG 59.644 44.000 0.00 0.00 0.00 3.06
1857 2028 0.397941 AGCTAGCTGGTTTGTGCTGA 59.602 50.000 18.57 0.00 40.08 4.26
1932 2103 3.284711 GGAGACGGAGGAGGAGAAA 57.715 57.895 0.00 0.00 0.00 2.52
2110 2284 3.350219 ACACCAACTACATGATGGACC 57.650 47.619 15.11 0.00 40.62 4.46
2168 2348 2.890311 AGTTCAGCTGATCCGGATAGAG 59.110 50.000 19.15 17.07 0.00 2.43
2191 2371 2.808543 GGGTGAAAGAACAGTGCTAGTG 59.191 50.000 0.00 0.00 0.00 2.74
2205 2385 5.749109 CAGTGCTAGTGGTAGTTTACTATGC 59.251 44.000 0.00 0.00 0.00 3.14
2275 2455 3.542690 CGTATGCACGTACTAGCAGTAG 58.457 50.000 13.37 4.94 44.94 2.57
2276 2456 3.002042 CGTATGCACGTACTAGCAGTAGT 59.998 47.826 13.37 1.66 44.94 2.73
2277 2457 4.209911 CGTATGCACGTACTAGCAGTAGTA 59.790 45.833 13.37 0.86 44.94 1.82
2294 2474 3.037431 AGTAGCAGCAAGTCAGAACTG 57.963 47.619 0.00 0.00 35.36 3.16
2295 2475 2.072298 GTAGCAGCAAGTCAGAACTGG 58.928 52.381 0.00 0.00 35.36 4.00
2355 2578 6.923928 AACGGAGAATCTCAGTAGTAGTAC 57.076 41.667 15.88 0.00 37.88 2.73
2356 2579 5.049167 ACGGAGAATCTCAGTAGTAGTACG 58.951 45.833 14.13 5.60 37.16 3.67
2357 2580 5.049167 CGGAGAATCTCAGTAGTAGTACGT 58.951 45.833 12.79 0.00 32.19 3.57
2358 2581 6.183360 ACGGAGAATCTCAGTAGTAGTACGTA 60.183 42.308 14.13 0.00 37.16 3.57
2359 2582 6.143758 CGGAGAATCTCAGTAGTAGTACGTAC 59.856 46.154 18.10 18.10 32.19 3.67
2360 2583 7.209475 GGAGAATCTCAGTAGTAGTACGTACT 58.791 42.308 29.62 29.62 39.52 2.73
2361 2584 8.356657 GGAGAATCTCAGTAGTAGTACGTACTA 58.643 40.741 27.51 27.51 38.03 1.82
2449 2700 3.684305 TCATGCAAGTGGTTTATCGTGAG 59.316 43.478 0.00 0.00 0.00 3.51
2460 2711 5.416639 TGGTTTATCGTGAGCTGAACTAGTA 59.583 40.000 0.00 0.00 0.00 1.82
2461 2712 5.972382 GGTTTATCGTGAGCTGAACTAGTAG 59.028 44.000 0.00 0.00 0.00 2.57
2462 2713 6.404513 GGTTTATCGTGAGCTGAACTAGTAGT 60.405 42.308 0.00 0.00 0.00 2.73
2463 2714 7.201679 GGTTTATCGTGAGCTGAACTAGTAGTA 60.202 40.741 2.50 0.00 0.00 1.82
2475 2726 7.382759 GCTGAACTAGTAGTAATGTCTAATGGC 59.617 40.741 2.50 0.00 0.00 4.40
2486 2737 1.594862 GTCTAATGGCGTGATCACAGC 59.405 52.381 24.93 24.92 0.00 4.40
2532 2844 6.709846 CCCCATTTGTATTCTTTTGCTTTTGA 59.290 34.615 0.00 0.00 0.00 2.69
2534 2846 8.231837 CCCATTTGTATTCTTTTGCTTTTGATG 58.768 33.333 0.00 0.00 0.00 3.07
2535 2847 8.991026 CCATTTGTATTCTTTTGCTTTTGATGA 58.009 29.630 0.00 0.00 0.00 2.92
2538 2850 9.761504 TTTGTATTCTTTTGCTTTTGATGATGA 57.238 25.926 0.00 0.00 0.00 2.92
2539 2851 9.932207 TTGTATTCTTTTGCTTTTGATGATGAT 57.068 25.926 0.00 0.00 0.00 2.45
2540 2852 9.577110 TGTATTCTTTTGCTTTTGATGATGATC 57.423 29.630 0.00 0.00 0.00 2.92
2542 2854 8.703604 ATTCTTTTGCTTTTGATGATGATCTG 57.296 30.769 0.00 0.00 0.00 2.90
2547 3335 3.317430 GCTTTTGATGATGATCTGGGGTC 59.683 47.826 0.00 0.00 0.00 4.46
2551 3339 1.772819 ATGATGATCTGGGGTCGGCC 61.773 60.000 0.00 0.00 0.00 6.13
2585 3373 1.973812 GGGCTTCACCTCAGTTGGC 60.974 63.158 0.00 0.00 39.10 4.52
2609 3398 6.128526 GCGGGCTTTATCACAGAAGAATATAC 60.129 42.308 0.00 0.00 0.00 1.47
2640 3429 1.106285 GGGAAATGCCACCTGATGAC 58.894 55.000 0.00 0.00 38.95 3.06
2648 3437 1.748591 GCCACCTGATGACATCCCTTC 60.749 57.143 12.90 0.00 0.00 3.46
2666 3455 1.442769 TCCGTCTTTCAATCAGCAGC 58.557 50.000 0.00 0.00 0.00 5.25
2675 3464 2.696506 TCAATCAGCAGCTGTTCTCTG 58.303 47.619 22.10 13.71 32.61 3.35
2681 3470 0.585357 GCAGCTGTTCTCTGTGTGTG 59.415 55.000 16.64 0.00 34.21 3.82
2682 3471 1.945387 CAGCTGTTCTCTGTGTGTGT 58.055 50.000 5.25 0.00 0.00 3.72
2683 3472 2.803133 GCAGCTGTTCTCTGTGTGTGTA 60.803 50.000 16.64 0.00 34.21 2.90
2684 3473 3.055591 CAGCTGTTCTCTGTGTGTGTAG 58.944 50.000 5.25 0.00 0.00 2.74
2685 3474 2.959030 AGCTGTTCTCTGTGTGTGTAGA 59.041 45.455 0.00 0.00 0.00 2.59
2686 3475 3.384789 AGCTGTTCTCTGTGTGTGTAGAA 59.615 43.478 0.00 0.00 0.00 2.10
2687 3476 3.738282 GCTGTTCTCTGTGTGTGTAGAAG 59.262 47.826 0.00 0.00 0.00 2.85
2688 3477 4.737946 GCTGTTCTCTGTGTGTGTAGAAGT 60.738 45.833 0.00 0.00 0.00 3.01
2689 3478 4.682787 TGTTCTCTGTGTGTGTAGAAGTG 58.317 43.478 0.00 0.00 0.00 3.16
2690 3479 3.371102 TCTCTGTGTGTGTAGAAGTGC 57.629 47.619 0.00 0.00 0.00 4.40
2691 3480 2.693074 TCTCTGTGTGTGTAGAAGTGCA 59.307 45.455 0.00 0.00 0.00 4.57
2692 3481 3.321968 TCTCTGTGTGTGTAGAAGTGCAT 59.678 43.478 0.00 0.00 0.00 3.96
2693 3482 3.392882 TCTGTGTGTGTAGAAGTGCATG 58.607 45.455 0.00 0.00 0.00 4.06
2694 3483 1.872952 TGTGTGTGTAGAAGTGCATGC 59.127 47.619 11.82 11.82 0.00 4.06
2695 3484 2.146342 GTGTGTGTAGAAGTGCATGCT 58.854 47.619 20.33 0.00 0.00 3.79
2696 3485 2.158449 GTGTGTGTAGAAGTGCATGCTC 59.842 50.000 20.33 15.94 0.00 4.26
2697 3486 2.037641 TGTGTGTAGAAGTGCATGCTCT 59.962 45.455 20.33 18.23 0.00 4.09
2698 3487 2.670414 GTGTGTAGAAGTGCATGCTCTC 59.330 50.000 21.65 14.76 0.00 3.20
2699 3488 2.299867 TGTGTAGAAGTGCATGCTCTCA 59.700 45.455 21.65 12.78 0.00 3.27
2700 3489 2.928757 GTGTAGAAGTGCATGCTCTCAG 59.071 50.000 21.65 0.00 0.00 3.35
2701 3490 2.093816 TGTAGAAGTGCATGCTCTCAGG 60.094 50.000 21.65 0.00 0.00 3.86
2707 3496 3.483954 GCATGCTCTCAGGCCTAAA 57.516 52.632 11.37 0.00 43.58 1.85
2708 3497 1.020437 GCATGCTCTCAGGCCTAAAC 58.980 55.000 11.37 0.00 43.58 2.01
2709 3498 1.679944 GCATGCTCTCAGGCCTAAACA 60.680 52.381 11.37 0.00 43.58 2.83
2710 3499 2.928334 CATGCTCTCAGGCCTAAACAT 58.072 47.619 3.98 2.20 0.00 2.71
2711 3500 2.408271 TGCTCTCAGGCCTAAACATG 57.592 50.000 3.98 0.00 0.00 3.21
2712 3501 1.065199 TGCTCTCAGGCCTAAACATGG 60.065 52.381 3.98 0.00 0.00 3.66
2713 3502 1.210478 GCTCTCAGGCCTAAACATGGA 59.790 52.381 3.98 0.00 0.00 3.41
2714 3503 2.911484 CTCTCAGGCCTAAACATGGAC 58.089 52.381 3.98 0.00 0.00 4.02
2715 3504 1.559682 TCTCAGGCCTAAACATGGACC 59.440 52.381 3.98 0.00 31.51 4.46
2716 3505 0.251916 TCAGGCCTAAACATGGACCG 59.748 55.000 3.98 0.00 31.51 4.79
2717 3506 0.251916 CAGGCCTAAACATGGACCGA 59.748 55.000 3.98 0.00 31.51 4.69
2718 3507 0.988832 AGGCCTAAACATGGACCGAA 59.011 50.000 1.29 0.00 31.51 4.30
2719 3508 1.353022 AGGCCTAAACATGGACCGAAA 59.647 47.619 1.29 0.00 31.51 3.46
2720 3509 2.164338 GGCCTAAACATGGACCGAAAA 58.836 47.619 0.00 0.00 0.00 2.29
2721 3510 2.758423 GGCCTAAACATGGACCGAAAAT 59.242 45.455 0.00 0.00 0.00 1.82
2722 3511 3.949113 GGCCTAAACATGGACCGAAAATA 59.051 43.478 0.00 0.00 0.00 1.40
2723 3512 4.036380 GGCCTAAACATGGACCGAAAATAG 59.964 45.833 0.00 0.00 0.00 1.73
2724 3513 4.638865 GCCTAAACATGGACCGAAAATAGT 59.361 41.667 0.00 0.00 0.00 2.12
2725 3514 5.124936 GCCTAAACATGGACCGAAAATAGTT 59.875 40.000 0.00 0.00 0.00 2.24
2726 3515 6.316890 GCCTAAACATGGACCGAAAATAGTTA 59.683 38.462 0.00 0.00 0.00 2.24
2727 3516 7.677982 GCCTAAACATGGACCGAAAATAGTTAC 60.678 40.741 0.00 0.00 0.00 2.50
2728 3517 7.334921 CCTAAACATGGACCGAAAATAGTTACA 59.665 37.037 0.00 0.00 0.00 2.41
2729 3518 6.737254 AACATGGACCGAAAATAGTTACAG 57.263 37.500 0.00 0.00 0.00 2.74
2730 3519 4.634443 ACATGGACCGAAAATAGTTACAGC 59.366 41.667 0.00 0.00 0.00 4.40
2731 3520 3.602483 TGGACCGAAAATAGTTACAGCC 58.398 45.455 0.00 0.00 0.00 4.85
2732 3521 3.008157 TGGACCGAAAATAGTTACAGCCA 59.992 43.478 0.00 0.00 0.00 4.75
2733 3522 3.621715 GGACCGAAAATAGTTACAGCCAG 59.378 47.826 0.00 0.00 0.00 4.85
2734 3523 3.007635 ACCGAAAATAGTTACAGCCAGC 58.992 45.455 0.00 0.00 0.00 4.85
2735 3524 3.270877 CCGAAAATAGTTACAGCCAGCT 58.729 45.455 0.00 0.00 0.00 4.24
2744 3533 2.752358 CAGCCAGCTGGGTCTTGA 59.248 61.111 34.15 0.00 45.47 3.02
2745 3534 1.073722 CAGCCAGCTGGGTCTTGAA 59.926 57.895 34.15 0.00 45.47 2.69
2746 3535 1.073897 AGCCAGCTGGGTCTTGAAC 59.926 57.895 31.61 13.01 43.48 3.18
2747 3536 1.073897 GCCAGCTGGGTCTTGAACT 59.926 57.895 33.46 0.00 39.65 3.01
2748 3537 0.538287 GCCAGCTGGGTCTTGAACTT 60.538 55.000 33.46 0.00 39.65 2.66
2749 3538 1.271379 GCCAGCTGGGTCTTGAACTTA 60.271 52.381 33.46 0.00 39.65 2.24
2750 3539 2.814097 GCCAGCTGGGTCTTGAACTTAA 60.814 50.000 33.46 0.00 39.65 1.85
2751 3540 3.077359 CCAGCTGGGTCTTGAACTTAAG 58.923 50.000 26.14 0.00 0.00 1.85
2752 3541 3.244561 CCAGCTGGGTCTTGAACTTAAGA 60.245 47.826 26.14 0.00 34.46 2.10
2762 3551 7.555306 GTCTTGAACTTAAGACCTTTTGACT 57.445 36.000 10.09 0.00 46.84 3.41
2763 3552 7.631822 GTCTTGAACTTAAGACCTTTTGACTC 58.368 38.462 10.09 0.00 46.84 3.36
2764 3553 7.496263 GTCTTGAACTTAAGACCTTTTGACTCT 59.504 37.037 10.09 0.00 46.84 3.24
2765 3554 7.495934 TCTTGAACTTAAGACCTTTTGACTCTG 59.504 37.037 10.09 0.00 32.02 3.35
2766 3555 6.884832 TGAACTTAAGACCTTTTGACTCTGA 58.115 36.000 10.09 0.00 0.00 3.27
2767 3556 7.509546 TGAACTTAAGACCTTTTGACTCTGAT 58.490 34.615 10.09 0.00 0.00 2.90
2768 3557 8.647796 TGAACTTAAGACCTTTTGACTCTGATA 58.352 33.333 10.09 0.00 0.00 2.15
2769 3558 8.834749 AACTTAAGACCTTTTGACTCTGATAC 57.165 34.615 10.09 0.00 0.00 2.24
2770 3559 7.091443 ACTTAAGACCTTTTGACTCTGATACG 58.909 38.462 10.09 0.00 0.00 3.06
2771 3560 5.723672 AAGACCTTTTGACTCTGATACGA 57.276 39.130 0.00 0.00 0.00 3.43
2772 3561 5.923733 AGACCTTTTGACTCTGATACGAT 57.076 39.130 0.00 0.00 0.00 3.73
2773 3562 5.655488 AGACCTTTTGACTCTGATACGATG 58.345 41.667 0.00 0.00 0.00 3.84
2774 3563 5.186021 AGACCTTTTGACTCTGATACGATGT 59.814 40.000 0.00 0.00 0.00 3.06
2775 3564 6.377429 AGACCTTTTGACTCTGATACGATGTA 59.623 38.462 0.00 0.00 0.00 2.29
2776 3565 6.565234 ACCTTTTGACTCTGATACGATGTAG 58.435 40.000 0.00 0.00 0.00 2.74
2777 3566 6.377429 ACCTTTTGACTCTGATACGATGTAGA 59.623 38.462 0.00 0.00 0.00 2.59
2778 3567 7.093902 ACCTTTTGACTCTGATACGATGTAGAA 60.094 37.037 0.00 0.00 0.00 2.10
2779 3568 7.433719 CCTTTTGACTCTGATACGATGTAGAAG 59.566 40.741 0.00 0.00 0.00 2.85
2780 3569 7.392494 TTTGACTCTGATACGATGTAGAAGT 57.608 36.000 0.00 0.00 0.00 3.01
2781 3570 6.364945 TGACTCTGATACGATGTAGAAGTG 57.635 41.667 0.00 0.00 0.00 3.16
2782 3571 5.176407 ACTCTGATACGATGTAGAAGTGC 57.824 43.478 0.00 0.00 0.00 4.40
2783 3572 4.640647 ACTCTGATACGATGTAGAAGTGCA 59.359 41.667 0.00 0.00 0.00 4.57
2784 3573 5.300539 ACTCTGATACGATGTAGAAGTGCAT 59.699 40.000 0.00 0.00 0.00 3.96
2785 3574 5.523369 TCTGATACGATGTAGAAGTGCATG 58.477 41.667 0.00 0.00 0.00 4.06
2786 3575 4.051237 TGATACGATGTAGAAGTGCATGC 58.949 43.478 11.82 11.82 0.00 4.06
2787 3576 2.680312 ACGATGTAGAAGTGCATGCT 57.320 45.000 20.33 0.00 0.00 3.79
2788 3577 2.977914 ACGATGTAGAAGTGCATGCTT 58.022 42.857 20.33 5.44 0.00 3.91
2789 3578 3.338249 ACGATGTAGAAGTGCATGCTTT 58.662 40.909 20.33 13.27 0.00 3.51
2790 3579 4.503910 ACGATGTAGAAGTGCATGCTTTA 58.496 39.130 20.33 0.00 0.00 1.85
2791 3580 4.568359 ACGATGTAGAAGTGCATGCTTTAG 59.432 41.667 20.33 0.72 0.00 1.85
2792 3581 4.568359 CGATGTAGAAGTGCATGCTTTAGT 59.432 41.667 20.33 0.00 0.00 2.24
2793 3582 5.276584 CGATGTAGAAGTGCATGCTTTAGTC 60.277 44.000 20.33 9.03 0.00 2.59
2794 3583 4.893608 TGTAGAAGTGCATGCTTTAGTCA 58.106 39.130 20.33 7.45 0.00 3.41
2795 3584 5.304778 TGTAGAAGTGCATGCTTTAGTCAA 58.695 37.500 20.33 0.00 0.00 3.18
2796 3585 5.939883 TGTAGAAGTGCATGCTTTAGTCAAT 59.060 36.000 20.33 0.00 0.00 2.57
2797 3586 5.306532 AGAAGTGCATGCTTTAGTCAATG 57.693 39.130 20.33 0.00 0.00 2.82
2798 3587 3.498927 AGTGCATGCTTTAGTCAATGC 57.501 42.857 20.33 0.00 35.82 3.56
2799 3588 2.821378 AGTGCATGCTTTAGTCAATGCA 59.179 40.909 20.33 5.13 45.57 3.96
2800 3589 3.256383 AGTGCATGCTTTAGTCAATGCAA 59.744 39.130 20.33 0.00 44.92 4.08
2801 3590 4.081862 AGTGCATGCTTTAGTCAATGCAAT 60.082 37.500 20.33 7.14 44.92 3.56
2802 3591 4.266976 GTGCATGCTTTAGTCAATGCAATC 59.733 41.667 20.33 0.00 44.92 2.67
2803 3592 4.082136 TGCATGCTTTAGTCAATGCAATCA 60.082 37.500 20.33 2.77 44.92 2.57
2804 3593 4.865925 GCATGCTTTAGTCAATGCAATCAA 59.134 37.500 11.37 0.00 44.92 2.57
2805 3594 5.349270 GCATGCTTTAGTCAATGCAATCAAA 59.651 36.000 11.37 0.00 44.92 2.69
2806 3595 6.455113 GCATGCTTTAGTCAATGCAATCAAAG 60.455 38.462 11.37 0.00 44.92 2.77
2807 3596 6.330004 TGCTTTAGTCAATGCAATCAAAGA 57.670 33.333 0.00 0.00 40.65 2.52
2808 3597 6.151691 TGCTTTAGTCAATGCAATCAAAGAC 58.848 36.000 0.00 0.00 40.65 3.01
2809 3598 5.574443 GCTTTAGTCAATGCAATCAAAGACC 59.426 40.000 0.00 0.00 35.46 3.85
2810 3599 3.837213 AGTCAATGCAATCAAAGACCG 57.163 42.857 0.00 0.00 33.33 4.79
2811 3600 3.411446 AGTCAATGCAATCAAAGACCGA 58.589 40.909 0.00 0.00 33.33 4.69
2812 3601 4.012374 AGTCAATGCAATCAAAGACCGAT 58.988 39.130 0.00 0.00 33.33 4.18
2813 3602 4.460382 AGTCAATGCAATCAAAGACCGATT 59.540 37.500 0.00 0.00 33.33 3.34
2814 3603 5.047802 AGTCAATGCAATCAAAGACCGATTT 60.048 36.000 0.00 0.00 33.33 2.17
2815 3604 5.061311 GTCAATGCAATCAAAGACCGATTTG 59.939 40.000 0.00 0.00 40.75 2.32
2853 3642 9.320352 ACTATGCAATACATTTATACGTCAACA 57.680 29.630 0.00 0.00 40.38 3.33
2856 3645 8.833976 TGCAATACATTTATACGTCAACAATG 57.166 30.769 0.00 0.00 0.00 2.82
2857 3646 8.454894 TGCAATACATTTATACGTCAACAATGT 58.545 29.630 15.49 15.49 40.38 2.71
2858 3647 8.733128 GCAATACATTTATACGTCAACAATGTG 58.267 33.333 18.45 8.71 38.30 3.21
2859 3648 9.767684 CAATACATTTATACGTCAACAATGTGT 57.232 29.630 18.45 12.62 38.30 3.72
2876 3665 1.741770 GTAACTGGCGGCACAGGAG 60.742 63.158 7.97 0.00 42.75 3.69
2901 3694 0.321034 CAGCACTAGCAAGGCACTGA 60.321 55.000 0.00 0.00 45.49 3.41
2902 3695 0.321122 AGCACTAGCAAGGCACTGAC 60.321 55.000 0.00 0.00 45.49 3.51
2903 3696 1.630244 GCACTAGCAAGGCACTGACG 61.630 60.000 0.00 0.00 40.86 4.35
2904 3697 1.374758 ACTAGCAAGGCACTGACGC 60.375 57.895 0.00 0.00 40.86 5.19
2905 3698 1.079543 CTAGCAAGGCACTGACGCT 60.080 57.895 0.00 0.00 40.86 5.07
2906 3699 0.671781 CTAGCAAGGCACTGACGCTT 60.672 55.000 0.00 0.00 40.86 4.68
2994 3787 1.521423 GTACAGCTAGCCGCATAAACG 59.479 52.381 12.13 0.00 42.61 3.60
3041 3834 2.202324 GTCGGACGTGTCGAGCTC 60.202 66.667 2.73 2.73 37.31 4.09
3045 3838 2.179517 GACGTGTCGAGCTCAGGG 59.820 66.667 15.40 0.00 0.00 4.45
3088 3881 1.762370 TCCGGAGCTAATGATTGCAGA 59.238 47.619 0.00 0.00 0.00 4.26
3133 3932 1.586154 AAAAGCCATTCTCCCGCGTG 61.586 55.000 4.92 0.00 0.00 5.34
3173 3974 1.566018 GATAAAAGGCGGGCGATCGG 61.566 60.000 18.30 0.83 0.00 4.18
3220 4021 4.843827 ACTCCAAAGTAACACGTACGTACG 60.844 45.833 38.49 38.49 43.96 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.604202 CGTCGTGTCGTATGCGCC 61.604 66.667 4.18 0.00 38.14 6.53
102 107 2.042230 ATTAGTCGCGGGGGAGGT 60.042 61.111 6.13 0.00 0.00 3.85
216 221 3.296709 GACGGTGACATCCTGCGGT 62.297 63.158 0.00 0.00 0.00 5.68
233 238 1.135373 GCGTCCAGAACTCATTCTCGA 60.135 52.381 2.04 0.00 43.69 4.04
284 289 4.980805 TCCGCGCACACTTGTCCC 62.981 66.667 8.75 0.00 0.00 4.46
312 320 1.698506 CTAGGTCGATCTGGGCTTCT 58.301 55.000 8.91 0.00 0.00 2.85
345 353 1.615883 CGAGGATCTTCATCGTCCCAT 59.384 52.381 5.61 0.00 44.47 4.00
369 378 2.344441 CGACAACGTAAATGCATCGAGT 59.656 45.455 12.64 10.07 34.56 4.18
386 397 1.228215 TCGGTGGTGTAGTCCGACA 60.228 57.895 0.40 0.00 46.54 4.35
408 419 2.803030 TGCTAGACTACTTCCCGTCT 57.197 50.000 0.00 0.00 42.67 4.18
413 424 4.995124 TGAAACGATGCTAGACTACTTCC 58.005 43.478 0.00 0.00 0.00 3.46
440 466 8.734030 GCAAGTTCATACGATGCTAAATAAAAC 58.266 33.333 0.00 0.00 38.29 2.43
495 521 9.974980 ATACGGAAACATTTACAGTTCAAATTT 57.025 25.926 0.00 0.00 0.00 1.82
506 532 5.520022 ACGACACATACGGAAACATTTAC 57.480 39.130 0.00 0.00 34.93 2.01
508 534 5.007823 TGAAACGACACATACGGAAACATTT 59.992 36.000 0.00 0.00 34.93 2.32
574 652 0.740868 GTAGCGCTTCACCAGATGCA 60.741 55.000 18.68 0.00 43.12 3.96
577 655 0.460987 GCTGTAGCGCTTCACCAGAT 60.461 55.000 18.68 0.00 0.00 2.90
630 708 2.093783 GGTTTTAACGCACGAGGATGAG 59.906 50.000 0.00 0.00 0.00 2.90
631 709 2.070783 GGTTTTAACGCACGAGGATGA 58.929 47.619 0.00 0.00 0.00 2.92
639 717 4.666928 TCGAAATAGGGTTTTAACGCAC 57.333 40.909 11.52 0.00 43.53 5.34
644 726 3.065648 GCGGCATCGAAATAGGGTTTTAA 59.934 43.478 0.00 0.00 39.00 1.52
651 733 2.842208 TTTTGCGGCATCGAAATAGG 57.158 45.000 2.28 0.00 39.00 2.57
696 782 5.175859 ACATGCTTACTACGCACTGTAAAT 58.824 37.500 0.00 0.00 40.65 1.40
707 793 4.849111 GCTTGAGTGACATGCTTACTAC 57.151 45.455 0.00 0.00 43.40 2.73
735 821 0.739813 CAGGGTAAAAGCGACCGAGG 60.740 60.000 0.00 0.00 37.90 4.63
751 840 1.202348 GGAAAATGAAACGGGAGCAGG 59.798 52.381 0.00 0.00 0.00 4.85
778 867 6.916440 TCAGAGTAATCGTGTGCTAGTTTTA 58.084 36.000 0.00 0.00 0.00 1.52
802 913 5.417894 TCTGCCGGTAATAGTGATCGATAAT 59.582 40.000 1.90 0.00 0.00 1.28
803 914 4.763279 TCTGCCGGTAATAGTGATCGATAA 59.237 41.667 1.90 0.00 0.00 1.75
804 915 4.329392 TCTGCCGGTAATAGTGATCGATA 58.671 43.478 1.90 0.00 0.00 2.92
824 935 2.744166 CGCTGTGGATTGGTCATCATCT 60.744 50.000 0.00 0.00 32.79 2.90
833 944 2.741985 TGTCGCGCTGTGGATTGG 60.742 61.111 5.56 0.00 0.00 3.16
884 995 4.275196 GGAGTTGGGGCTTAATAATTCGTC 59.725 45.833 0.00 0.00 0.00 4.20
932 1046 0.821711 CTGAGGAGAGAGGGGCGTAG 60.822 65.000 0.00 0.00 0.00 3.51
935 1049 3.535962 GCTGAGGAGAGAGGGGCG 61.536 72.222 0.00 0.00 0.00 6.13
936 1050 3.160748 GGCTGAGGAGAGAGGGGC 61.161 72.222 0.00 0.00 0.00 5.80
1061 1190 1.598517 GATGCTTTGGGCTTTGGGG 59.401 57.895 0.00 0.00 42.39 4.96
1101 1231 4.442706 AGTGCCCGATCAACAAATACTAG 58.557 43.478 0.00 0.00 0.00 2.57
1118 1248 3.551846 ACTTCTCTCTCTAGCTAGTGCC 58.448 50.000 20.10 0.00 40.80 5.01
1183 1313 3.063197 GCCTCTCTCCCTCCTCGGA 62.063 68.421 0.00 0.00 33.16 4.55
1275 1405 4.379339 TCAACGACGACATGGATGATTA 57.621 40.909 0.00 0.00 0.00 1.75
1278 1408 2.959507 ATCAACGACGACATGGATGA 57.040 45.000 0.00 0.00 0.00 2.92
1279 1409 4.550831 GCTAAATCAACGACGACATGGATG 60.551 45.833 0.00 0.00 0.00 3.51
1321 1451 1.202043 ACTCGATCGAGCACTTACGTG 60.202 52.381 38.12 16.93 45.54 4.49
1327 1465 0.881796 TGAACACTCGATCGAGCACT 59.118 50.000 38.12 24.83 45.54 4.40
1378 1524 2.270205 CTCTCCGCCTGCACCATT 59.730 61.111 0.00 0.00 0.00 3.16
1389 1538 1.153469 GGCCTTCTTCTGCTCTCCG 60.153 63.158 0.00 0.00 0.00 4.63
1482 1634 4.778415 TCGTCGCTCAGCCTTCGC 62.778 66.667 0.00 0.00 0.00 4.70
1485 1637 3.639541 CTGCTCGTCGCTCAGCCTT 62.640 63.158 0.00 0.00 40.11 4.35
1486 1638 4.127040 CTGCTCGTCGCTCAGCCT 62.127 66.667 0.00 0.00 40.11 4.58
1523 1675 0.610687 CTTCCGCTCCTTCCTGAAGT 59.389 55.000 6.19 0.00 36.72 3.01
1644 1796 2.650322 GAGAACTCCTCCTCGATGAGT 58.350 52.381 15.38 8.64 38.74 3.41
1729 1881 2.486636 TAGCCAGTCGGACTGTTGCG 62.487 60.000 30.32 18.94 44.50 4.85
1816 1981 5.122082 GCTAGCTACGTATAGTACCCAAGAG 59.878 48.000 7.70 0.00 0.00 2.85
2067 2241 2.386501 CGTACTCGCTCATGTAGGTC 57.613 55.000 0.00 0.00 0.00 3.85
2160 2340 1.789523 TCTTTCACCCCCTCTATCCG 58.210 55.000 0.00 0.00 0.00 4.18
2168 2348 0.178990 AGCACTGTTCTTTCACCCCC 60.179 55.000 0.00 0.00 0.00 5.40
2191 2371 8.438676 ACATTGATTGAGCATAGTAAACTACC 57.561 34.615 0.00 0.00 0.00 3.18
2227 2407 1.953686 CCGCAATCCCGGTTGATTAAT 59.046 47.619 8.89 0.00 43.24 1.40
2275 2455 2.072298 CCAGTTCTGACTTGCTGCTAC 58.928 52.381 0.00 0.00 32.54 3.58
2276 2456 1.002430 CCCAGTTCTGACTTGCTGCTA 59.998 52.381 0.00 0.00 32.54 3.49
2277 2457 0.250640 CCCAGTTCTGACTTGCTGCT 60.251 55.000 0.00 0.00 32.54 4.24
2294 2474 5.425196 TGAAACTACCACCAATACTACCC 57.575 43.478 0.00 0.00 0.00 3.69
2295 2475 6.317893 CCATTGAAACTACCACCAATACTACC 59.682 42.308 0.00 0.00 0.00 3.18
2355 2578 5.751509 TGTACATGGCTTAGCAAATAGTACG 59.248 40.000 6.53 0.00 33.83 3.67
2356 2579 7.730364 ATGTACATGGCTTAGCAAATAGTAC 57.270 36.000 7.78 10.34 0.00 2.73
2358 2581 8.786898 CATAATGTACATGGCTTAGCAAATAGT 58.213 33.333 9.63 0.00 0.00 2.12
2359 2582 9.002600 TCATAATGTACATGGCTTAGCAAATAG 57.997 33.333 9.63 0.00 0.00 1.73
2360 2583 8.916628 TCATAATGTACATGGCTTAGCAAATA 57.083 30.769 9.63 0.00 0.00 1.40
2361 2584 7.822161 TCATAATGTACATGGCTTAGCAAAT 57.178 32.000 9.63 0.00 0.00 2.32
2409 2636 6.472016 TGCATGATGATAACCCGTACATAAT 58.528 36.000 0.00 0.00 0.00 1.28
2410 2637 5.859495 TGCATGATGATAACCCGTACATAA 58.141 37.500 0.00 0.00 0.00 1.90
2449 2700 7.382759 GCCATTAGACATTACTACTAGTTCAGC 59.617 40.741 0.00 0.00 0.00 4.26
2460 2711 5.050490 GTGATCACGCCATTAGACATTACT 58.950 41.667 10.69 0.00 0.00 2.24
2461 2712 4.808895 TGTGATCACGCCATTAGACATTAC 59.191 41.667 20.54 0.00 0.00 1.89
2462 2713 5.017294 TGTGATCACGCCATTAGACATTA 57.983 39.130 20.54 0.00 0.00 1.90
2463 2714 3.872696 TGTGATCACGCCATTAGACATT 58.127 40.909 20.54 0.00 0.00 2.71
2486 2737 0.723414 CTGCACATACGCCTTGTGAG 59.277 55.000 14.87 7.29 45.83 3.51
2532 2844 1.757306 GCCGACCCCAGATCATCAT 59.243 57.895 0.00 0.00 0.00 2.45
2534 2846 2.105806 GAGGCCGACCCCAGATCATC 62.106 65.000 0.00 0.00 36.11 2.92
2535 2847 2.040464 AGGCCGACCCCAGATCAT 60.040 61.111 0.00 0.00 36.11 2.45
2537 2849 3.917760 CGAGGCCGACCCCAGATC 61.918 72.222 0.00 0.00 38.22 2.75
2551 3339 2.046892 CCAGTCAGTTGGGCCGAG 60.047 66.667 0.00 0.00 34.46 4.63
2585 3373 7.155328 AGTATATTCTTCTGTGATAAAGCCCG 58.845 38.462 0.00 0.00 0.00 6.13
2609 3398 4.524328 GTGGCATTTCCCCCTTCATAATAG 59.476 45.833 0.00 0.00 0.00 1.73
2622 3411 1.838112 TGTCATCAGGTGGCATTTCC 58.162 50.000 0.00 0.00 37.56 3.13
2640 3429 3.609853 TGATTGAAAGACGGAAGGGATG 58.390 45.455 0.00 0.00 0.00 3.51
2648 3437 1.129998 CAGCTGCTGATTGAAAGACGG 59.870 52.381 24.88 0.00 32.44 4.79
2666 3455 4.742167 CACTTCTACACACACAGAGAACAG 59.258 45.833 0.00 0.00 0.00 3.16
2675 3464 2.146342 AGCATGCACTTCTACACACAC 58.854 47.619 21.98 0.00 0.00 3.82
2681 3470 2.548875 CCTGAGAGCATGCACTTCTAC 58.451 52.381 21.98 7.52 0.00 2.59
2682 3471 1.134580 GCCTGAGAGCATGCACTTCTA 60.135 52.381 21.98 8.74 35.94 2.10
2683 3472 0.392729 GCCTGAGAGCATGCACTTCT 60.393 55.000 21.98 14.27 35.94 2.85
2684 3473 1.375098 GGCCTGAGAGCATGCACTTC 61.375 60.000 21.98 14.14 37.39 3.01
2685 3474 1.378250 GGCCTGAGAGCATGCACTT 60.378 57.895 21.98 4.17 37.39 3.16
2686 3475 0.979709 TAGGCCTGAGAGCATGCACT 60.980 55.000 21.98 19.96 37.39 4.40
2687 3476 0.107508 TTAGGCCTGAGAGCATGCAC 60.108 55.000 21.98 14.59 37.39 4.57
2688 3477 0.620030 TTTAGGCCTGAGAGCATGCA 59.380 50.000 21.98 0.00 37.39 3.96
2689 3478 1.020437 GTTTAGGCCTGAGAGCATGC 58.980 55.000 17.99 10.51 35.25 4.06
2690 3479 2.408271 TGTTTAGGCCTGAGAGCATG 57.592 50.000 17.99 0.00 0.00 4.06
2691 3480 2.422519 CCATGTTTAGGCCTGAGAGCAT 60.423 50.000 17.99 11.96 0.00 3.79
2692 3481 1.065199 CCATGTTTAGGCCTGAGAGCA 60.065 52.381 17.99 10.02 0.00 4.26
2693 3482 1.210478 TCCATGTTTAGGCCTGAGAGC 59.790 52.381 17.99 3.93 0.00 4.09
2694 3483 2.420687 GGTCCATGTTTAGGCCTGAGAG 60.421 54.545 17.99 0.00 0.00 3.20
2695 3484 1.559682 GGTCCATGTTTAGGCCTGAGA 59.440 52.381 17.99 2.38 0.00 3.27
2696 3485 1.743772 CGGTCCATGTTTAGGCCTGAG 60.744 57.143 17.99 0.00 0.00 3.35
2697 3486 0.251916 CGGTCCATGTTTAGGCCTGA 59.748 55.000 17.99 3.42 0.00 3.86
2698 3487 0.251916 TCGGTCCATGTTTAGGCCTG 59.748 55.000 17.99 0.00 0.00 4.85
2699 3488 0.988832 TTCGGTCCATGTTTAGGCCT 59.011 50.000 11.78 11.78 0.00 5.19
2700 3489 1.828979 TTTCGGTCCATGTTTAGGCC 58.171 50.000 0.00 0.00 0.00 5.19
2701 3490 4.638865 ACTATTTTCGGTCCATGTTTAGGC 59.361 41.667 0.00 0.00 0.00 3.93
2702 3491 6.753107 AACTATTTTCGGTCCATGTTTAGG 57.247 37.500 0.00 0.00 0.00 2.69
2703 3492 8.259049 TGTAACTATTTTCGGTCCATGTTTAG 57.741 34.615 0.00 0.00 0.00 1.85
2704 3493 7.148373 GCTGTAACTATTTTCGGTCCATGTTTA 60.148 37.037 0.00 0.00 0.00 2.01
2705 3494 6.349033 GCTGTAACTATTTTCGGTCCATGTTT 60.349 38.462 0.00 0.00 0.00 2.83
2706 3495 5.123344 GCTGTAACTATTTTCGGTCCATGTT 59.877 40.000 0.00 0.00 0.00 2.71
2707 3496 4.634443 GCTGTAACTATTTTCGGTCCATGT 59.366 41.667 0.00 0.00 0.00 3.21
2708 3497 4.035208 GGCTGTAACTATTTTCGGTCCATG 59.965 45.833 0.00 0.00 0.00 3.66
2709 3498 4.196971 GGCTGTAACTATTTTCGGTCCAT 58.803 43.478 0.00 0.00 0.00 3.41
2710 3499 3.008157 TGGCTGTAACTATTTTCGGTCCA 59.992 43.478 0.00 0.00 0.00 4.02
2711 3500 3.602483 TGGCTGTAACTATTTTCGGTCC 58.398 45.455 0.00 0.00 0.00 4.46
2712 3501 3.063588 GCTGGCTGTAACTATTTTCGGTC 59.936 47.826 0.00 0.00 0.00 4.79
2713 3502 3.007635 GCTGGCTGTAACTATTTTCGGT 58.992 45.455 0.00 0.00 0.00 4.69
2714 3503 3.063997 CAGCTGGCTGTAACTATTTTCGG 59.936 47.826 13.76 0.00 39.10 4.30
2715 3504 3.063997 CCAGCTGGCTGTAACTATTTTCG 59.936 47.826 22.33 0.00 42.15 3.46
2716 3505 3.378427 CCCAGCTGGCTGTAACTATTTTC 59.622 47.826 28.39 0.00 42.15 2.29
2717 3506 3.245264 ACCCAGCTGGCTGTAACTATTTT 60.245 43.478 28.39 0.00 42.15 1.82
2718 3507 2.308866 ACCCAGCTGGCTGTAACTATTT 59.691 45.455 28.39 0.00 42.15 1.40
2719 3508 1.916181 ACCCAGCTGGCTGTAACTATT 59.084 47.619 28.39 0.00 42.15 1.73
2720 3509 1.486726 GACCCAGCTGGCTGTAACTAT 59.513 52.381 28.39 2.95 42.15 2.12
2721 3510 0.902531 GACCCAGCTGGCTGTAACTA 59.097 55.000 28.39 0.00 42.15 2.24
2722 3511 0.838122 AGACCCAGCTGGCTGTAACT 60.838 55.000 28.39 14.98 42.15 2.24
2723 3512 0.036875 AAGACCCAGCTGGCTGTAAC 59.963 55.000 28.39 13.06 42.15 2.50
2724 3513 0.036732 CAAGACCCAGCTGGCTGTAA 59.963 55.000 28.39 0.00 42.15 2.41
2725 3514 0.835971 TCAAGACCCAGCTGGCTGTA 60.836 55.000 28.39 8.81 42.15 2.74
2726 3515 1.708993 TTCAAGACCCAGCTGGCTGT 61.709 55.000 28.39 20.64 42.15 4.40
2727 3516 1.073722 TTCAAGACCCAGCTGGCTG 59.926 57.895 28.39 19.45 43.26 4.85
2728 3517 1.073897 GTTCAAGACCCAGCTGGCT 59.926 57.895 28.39 14.97 37.83 4.75
2729 3518 0.538287 AAGTTCAAGACCCAGCTGGC 60.538 55.000 28.39 14.93 37.83 4.85
2730 3519 2.859165 TAAGTTCAAGACCCAGCTGG 57.141 50.000 26.87 26.87 41.37 4.85
2731 3520 3.748568 GTCTTAAGTTCAAGACCCAGCTG 59.251 47.826 6.78 6.78 45.75 4.24
2732 3521 4.009370 GTCTTAAGTTCAAGACCCAGCT 57.991 45.455 1.63 0.00 45.75 4.24
2739 3528 7.495934 CAGAGTCAAAAGGTCTTAAGTTCAAGA 59.504 37.037 1.63 0.00 32.11 3.02
2740 3529 7.495934 TCAGAGTCAAAAGGTCTTAAGTTCAAG 59.504 37.037 1.63 0.00 0.00 3.02
2741 3530 7.335627 TCAGAGTCAAAAGGTCTTAAGTTCAA 58.664 34.615 1.63 0.00 0.00 2.69
2742 3531 6.884832 TCAGAGTCAAAAGGTCTTAAGTTCA 58.115 36.000 1.63 0.00 0.00 3.18
2743 3532 7.971183 ATCAGAGTCAAAAGGTCTTAAGTTC 57.029 36.000 1.63 0.00 0.00 3.01
2744 3533 7.599245 CGTATCAGAGTCAAAAGGTCTTAAGTT 59.401 37.037 1.63 0.00 0.00 2.66
2745 3534 7.039923 TCGTATCAGAGTCAAAAGGTCTTAAGT 60.040 37.037 1.63 0.00 0.00 2.24
2746 3535 7.313646 TCGTATCAGAGTCAAAAGGTCTTAAG 58.686 38.462 0.00 0.00 0.00 1.85
2747 3536 7.223260 TCGTATCAGAGTCAAAAGGTCTTAA 57.777 36.000 0.00 0.00 0.00 1.85
2748 3537 6.829229 TCGTATCAGAGTCAAAAGGTCTTA 57.171 37.500 0.00 0.00 0.00 2.10
2749 3538 5.723672 TCGTATCAGAGTCAAAAGGTCTT 57.276 39.130 0.00 0.00 0.00 3.01
2750 3539 5.186021 ACATCGTATCAGAGTCAAAAGGTCT 59.814 40.000 0.00 0.00 0.00 3.85
2751 3540 5.411781 ACATCGTATCAGAGTCAAAAGGTC 58.588 41.667 0.00 0.00 0.00 3.85
2752 3541 5.407407 ACATCGTATCAGAGTCAAAAGGT 57.593 39.130 0.00 0.00 0.00 3.50
2753 3542 6.796426 TCTACATCGTATCAGAGTCAAAAGG 58.204 40.000 0.00 0.00 0.00 3.11
2754 3543 7.971168 ACTTCTACATCGTATCAGAGTCAAAAG 59.029 37.037 0.00 0.00 0.00 2.27
2755 3544 7.755373 CACTTCTACATCGTATCAGAGTCAAAA 59.245 37.037 0.00 0.00 0.00 2.44
2756 3545 7.251281 CACTTCTACATCGTATCAGAGTCAAA 58.749 38.462 0.00 0.00 0.00 2.69
2757 3546 6.678164 GCACTTCTACATCGTATCAGAGTCAA 60.678 42.308 0.00 0.00 0.00 3.18
2758 3547 5.220873 GCACTTCTACATCGTATCAGAGTCA 60.221 44.000 0.00 0.00 0.00 3.41
2759 3548 5.209240 GCACTTCTACATCGTATCAGAGTC 58.791 45.833 0.00 0.00 0.00 3.36
2760 3549 4.640647 TGCACTTCTACATCGTATCAGAGT 59.359 41.667 0.00 0.00 0.00 3.24
2761 3550 5.175090 TGCACTTCTACATCGTATCAGAG 57.825 43.478 0.00 0.00 0.00 3.35
2762 3551 5.523369 CATGCACTTCTACATCGTATCAGA 58.477 41.667 0.00 0.00 0.00 3.27
2763 3552 4.149571 GCATGCACTTCTACATCGTATCAG 59.850 45.833 14.21 0.00 0.00 2.90
2764 3553 4.051237 GCATGCACTTCTACATCGTATCA 58.949 43.478 14.21 0.00 0.00 2.15
2765 3554 4.302455 AGCATGCACTTCTACATCGTATC 58.698 43.478 21.98 0.00 0.00 2.24
2766 3555 4.327982 AGCATGCACTTCTACATCGTAT 57.672 40.909 21.98 0.00 0.00 3.06
2767 3556 3.801114 AGCATGCACTTCTACATCGTA 57.199 42.857 21.98 0.00 0.00 3.43
2768 3557 2.680312 AGCATGCACTTCTACATCGT 57.320 45.000 21.98 0.00 0.00 3.73
2769 3558 4.568359 ACTAAAGCATGCACTTCTACATCG 59.432 41.667 21.98 0.00 0.00 3.84
2770 3559 5.582269 TGACTAAAGCATGCACTTCTACATC 59.418 40.000 21.98 5.95 0.00 3.06
2771 3560 5.491070 TGACTAAAGCATGCACTTCTACAT 58.509 37.500 21.98 0.00 0.00 2.29
2772 3561 4.893608 TGACTAAAGCATGCACTTCTACA 58.106 39.130 21.98 8.71 0.00 2.74
2773 3562 5.862924 TTGACTAAAGCATGCACTTCTAC 57.137 39.130 21.98 6.13 0.00 2.59
2774 3563 5.163723 GCATTGACTAAAGCATGCACTTCTA 60.164 40.000 21.98 5.99 35.35 2.10
2775 3564 4.380233 GCATTGACTAAAGCATGCACTTCT 60.380 41.667 21.98 0.00 35.35 2.85
2776 3565 3.855950 GCATTGACTAAAGCATGCACTTC 59.144 43.478 21.98 8.98 35.35 3.01
2777 3566 3.256383 TGCATTGACTAAAGCATGCACTT 59.744 39.130 21.98 14.92 39.69 3.16
2778 3567 2.821378 TGCATTGACTAAAGCATGCACT 59.179 40.909 21.98 8.71 39.69 4.40
2779 3568 3.220507 TGCATTGACTAAAGCATGCAC 57.779 42.857 21.98 4.43 39.69 4.57
2780 3569 3.938289 TTGCATTGACTAAAGCATGCA 57.062 38.095 21.98 1.57 42.36 3.96
2781 3570 4.426416 TGATTGCATTGACTAAAGCATGC 58.574 39.130 10.51 10.51 36.80 4.06
2782 3571 6.809689 TCTTTGATTGCATTGACTAAAGCATG 59.190 34.615 0.00 0.00 36.80 4.06
2783 3572 6.810182 GTCTTTGATTGCATTGACTAAAGCAT 59.190 34.615 0.00 0.00 36.80 3.79
2784 3573 6.151691 GTCTTTGATTGCATTGACTAAAGCA 58.848 36.000 0.00 0.00 34.79 3.91
2785 3574 5.574443 GGTCTTTGATTGCATTGACTAAAGC 59.426 40.000 0.00 0.00 31.56 3.51
2786 3575 5.796935 CGGTCTTTGATTGCATTGACTAAAG 59.203 40.000 0.00 0.00 31.56 1.85
2787 3576 5.471797 TCGGTCTTTGATTGCATTGACTAAA 59.528 36.000 0.00 0.00 31.56 1.85
2788 3577 5.000591 TCGGTCTTTGATTGCATTGACTAA 58.999 37.500 0.00 0.00 31.56 2.24
2789 3578 4.574892 TCGGTCTTTGATTGCATTGACTA 58.425 39.130 0.00 0.00 31.56 2.59
2790 3579 3.411446 TCGGTCTTTGATTGCATTGACT 58.589 40.909 0.00 0.00 31.56 3.41
2791 3580 3.829886 TCGGTCTTTGATTGCATTGAC 57.170 42.857 0.00 0.00 0.00 3.18
2792 3581 5.048154 TCAAATCGGTCTTTGATTGCATTGA 60.048 36.000 0.00 0.00 39.55 2.57
2793 3582 5.162794 TCAAATCGGTCTTTGATTGCATTG 58.837 37.500 0.00 0.00 39.55 2.82
2794 3583 5.389859 TCAAATCGGTCTTTGATTGCATT 57.610 34.783 0.00 0.00 39.55 3.56
2827 3616 9.320352 TGTTGACGTATAAATGTATTGCATAGT 57.680 29.630 0.00 0.00 36.67 2.12
2830 3619 9.449550 CATTGTTGACGTATAAATGTATTGCAT 57.550 29.630 0.00 0.00 40.03 3.96
2831 3620 8.454894 ACATTGTTGACGTATAAATGTATTGCA 58.545 29.630 13.57 0.00 39.13 4.08
2832 3621 8.733128 CACATTGTTGACGTATAAATGTATTGC 58.267 33.333 14.36 0.00 38.94 3.56
2833 3622 9.767684 ACACATTGTTGACGTATAAATGTATTG 57.232 29.630 14.36 8.24 38.94 1.90
2837 3626 8.995220 AGTTACACATTGTTGACGTATAAATGT 58.005 29.630 10.77 10.77 41.01 2.71
2838 3627 9.261318 CAGTTACACATTGTTGACGTATAAATG 57.739 33.333 9.80 9.80 34.99 2.32
2839 3628 8.447833 CCAGTTACACATTGTTGACGTATAAAT 58.552 33.333 0.00 0.00 0.00 1.40
2840 3629 7.571613 GCCAGTTACACATTGTTGACGTATAAA 60.572 37.037 0.00 0.00 0.00 1.40
2841 3630 6.128499 GCCAGTTACACATTGTTGACGTATAA 60.128 38.462 0.00 0.00 0.00 0.98
2842 3631 5.349270 GCCAGTTACACATTGTTGACGTATA 59.651 40.000 0.00 0.00 0.00 1.47
2843 3632 4.153475 GCCAGTTACACATTGTTGACGTAT 59.847 41.667 0.00 0.00 0.00 3.06
2844 3633 3.495377 GCCAGTTACACATTGTTGACGTA 59.505 43.478 0.00 0.00 0.00 3.57
2845 3634 2.289547 GCCAGTTACACATTGTTGACGT 59.710 45.455 0.00 0.00 0.00 4.34
2846 3635 2.661709 CGCCAGTTACACATTGTTGACG 60.662 50.000 0.00 0.00 0.00 4.35
2847 3636 2.350388 CCGCCAGTTACACATTGTTGAC 60.350 50.000 0.00 0.00 0.00 3.18
2848 3637 1.876799 CCGCCAGTTACACATTGTTGA 59.123 47.619 0.00 0.00 0.00 3.18
2849 3638 1.665735 GCCGCCAGTTACACATTGTTG 60.666 52.381 0.00 0.00 0.00 3.33
2850 3639 0.596082 GCCGCCAGTTACACATTGTT 59.404 50.000 0.00 0.00 0.00 2.83
2851 3640 0.536233 TGCCGCCAGTTACACATTGT 60.536 50.000 0.00 0.00 0.00 2.71
2852 3641 0.109781 GTGCCGCCAGTTACACATTG 60.110 55.000 0.00 0.00 33.23 2.82
2853 3642 0.536233 TGTGCCGCCAGTTACACATT 60.536 50.000 0.00 0.00 38.07 2.71
2854 3643 0.955428 CTGTGCCGCCAGTTACACAT 60.955 55.000 0.00 0.00 41.80 3.21
2855 3644 1.596752 CTGTGCCGCCAGTTACACA 60.597 57.895 0.00 0.00 40.53 3.72
2856 3645 2.325082 CCTGTGCCGCCAGTTACAC 61.325 63.158 7.73 0.00 0.00 2.90
2857 3646 2.031919 CCTGTGCCGCCAGTTACA 59.968 61.111 7.73 0.00 0.00 2.41
2858 3647 1.741770 CTCCTGTGCCGCCAGTTAC 60.742 63.158 7.73 0.00 0.00 2.50
2859 3648 1.888436 CTCTCCTGTGCCGCCAGTTA 61.888 60.000 7.73 0.00 0.00 2.24
2860 3649 3.241530 TCTCCTGTGCCGCCAGTT 61.242 61.111 7.73 0.00 0.00 3.16
2882 3674 0.321034 TCAGTGCCTTGCTAGTGCTG 60.321 55.000 9.24 7.15 40.48 4.41
2904 3697 0.583438 CGAATGATGCCCAGCGTAAG 59.417 55.000 0.00 0.00 43.44 2.34
2905 3698 0.813610 CCGAATGATGCCCAGCGTAA 60.814 55.000 0.00 0.00 0.00 3.18
2906 3699 1.227527 CCGAATGATGCCCAGCGTA 60.228 57.895 0.00 0.00 0.00 4.42
2963 3756 0.729116 TAGCTGTACGTACGTGAGCC 59.271 55.000 33.23 22.41 36.31 4.70
3026 3819 2.202362 CTGAGCTCGACACGTCCG 60.202 66.667 9.64 0.82 0.00 4.79
3041 3834 0.521735 GCTGCGGTTTTTCTACCCTG 59.478 55.000 0.00 0.00 34.56 4.45
3045 3838 1.539827 ACATGGCTGCGGTTTTTCTAC 59.460 47.619 0.00 0.00 0.00 2.59
3088 3881 2.668550 GGCTGGTTCGGTTCGCTT 60.669 61.111 0.00 0.00 0.00 4.68
3113 3911 1.305930 ACGCGGGAGAATGGCTTTTC 61.306 55.000 12.47 0.00 0.00 2.29
3152 3953 1.228154 ATCGCCCGCCTTTTATCCC 60.228 57.895 0.00 0.00 0.00 3.85
3173 3974 1.876156 GATCCGTCATTTCATCCAGGC 59.124 52.381 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.