Multiple sequence alignment - TraesCS2D01G365400

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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 TraesCS2D01G365400 chr2D 100.000 4722 0 0 1 4722 470228678 470223957 0.000000e+00 8720
1 TraesCS2D01G365400 chr2D 96.875 128 4 0 2477 2604 552190019 552189892 1.030000e-51 215
2 TraesCS2D01G365400 chr2A 92.921 1554 79 13 787 2318 611957615 611956071 0.000000e+00 2231
3 TraesCS2D01G365400 chr2A 90.480 1166 79 17 2601 3745 611955969 611954815 0.000000e+00 1509
4 TraesCS2D01G365400 chr2A 92.701 411 13 6 329 723 611965462 611965053 1.140000e-160 577
5 TraesCS2D01G365400 chr2A 94.183 361 13 2 4162 4522 611954334 611953982 1.160000e-150 544
6 TraesCS2D01G365400 chr2A 90.966 321 23 4 2 319 611965872 611965555 1.210000e-115 427
7 TraesCS2D01G365400 chr2A 84.793 434 34 13 3736 4151 611954866 611954447 1.580000e-109 407
8 TraesCS2D01G365400 chr2A 96.023 176 7 0 4473 4648 611953965 611953790 2.150000e-73 287
9 TraesCS2D01G365400 chr2A 96.460 113 4 0 2370 2482 611956075 611955963 2.240000e-43 187
10 TraesCS2D01G365400 chr2B 91.595 1630 74 36 877 2482 549194737 549193147 0.000000e+00 2193
11 TraesCS2D01G365400 chr2B 92.778 997 37 8 3736 4722 549192341 549191370 0.000000e+00 1410
12 TraesCS2D01G365400 chr2B 94.527 402 16 4 2601 3001 549193153 549192757 2.410000e-172 616
13 TraesCS2D01G365400 chr2B 88.840 457 15 8 3291 3740 549192724 549192297 3.240000e-146 529
14 TraesCS2D01G365400 chr2B 89.070 430 10 11 330 724 549195335 549194908 2.540000e-137 499
15 TraesCS2D01G365400 chr2B 91.973 299 20 2 22 319 549195724 549195429 2.630000e-112 416
16 TraesCS2D01G365400 chrUn 97.619 126 3 0 2481 2606 48417754 48417629 2.860000e-52 217
17 TraesCS2D01G365400 chr7B 94.891 137 7 0 2469 2605 461475557 461475693 1.030000e-51 215
18 TraesCS2D01G365400 chr3D 96.850 127 4 0 2478 2604 267286409 267286535 3.700000e-51 213
19 TraesCS2D01G365400 chr7A 94.118 136 8 0 2470 2605 343843848 343843713 1.720000e-49 207
20 TraesCS2D01G365400 chr6B 93.571 140 7 1 2467 2604 86394318 86394457 1.720000e-49 207
21 TraesCS2D01G365400 chr3A 94.776 134 6 1 2471 2604 685017109 685017241 1.720000e-49 207
22 TraesCS2D01G365400 chr4B 93.478 138 9 0 2481 2618 306606570 306606433 6.190000e-49 206
23 TraesCS2D01G365400 chr6D 95.238 126 6 0 2481 2606 435990634 435990509 2.880000e-47 200


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 TraesCS2D01G365400 chr2D 470223957 470228678 4721 True 8720.000000 8720 100.000000 1 4722 1 chr2D.!!$R1 4721
1 TraesCS2D01G365400 chr2A 611953790 611957615 3825 True 860.833333 2231 92.476667 787 4648 6 chr2A.!!$R1 3861
2 TraesCS2D01G365400 chr2A 611965053 611965872 819 True 502.000000 577 91.833500 2 723 2 chr2A.!!$R2 721
3 TraesCS2D01G365400 chr2B 549191370 549195724 4354 True 943.833333 2193 91.463833 22 4722 6 chr2B.!!$R1 4700

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
253 255 0.034089 ACCTGCTGGAATGGGTAAGC 60.034 55.0 17.64 0.0 37.04 3.09 F
747 922 0.239347 GAATGTGTGAGTGTGCTGGC 59.761 55.0 0.00 0.0 0.00 4.85 F
2492 2720 0.042131 ACAGTAATCCCTCCGTCCCA 59.958 55.0 0.00 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 1482 0.610687 AGGAAGGCTTGAACTCCTCG 59.389 55.0 3.46 0.0 0.00 4.63 R
2588 2816 0.337082 TGAATACTCCCTCCGTCCCA 59.663 55.0 0.00 0.0 0.00 4.37 R
3739 3980 0.035630 ACTCCTCTGGCTGATGCAAC 60.036 55.0 0.00 0.0 41.91 4.17 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
226 228 1.382420 AGCCTCGCTCTCCAAGGAT 60.382 57.895 0.00 0.00 30.62 3.24
239 241 1.471676 CCAAGGATACAGACGACCTGC 60.472 57.143 8.95 0.00 46.81 4.85
242 244 0.103208 GGATACAGACGACCTGCTGG 59.897 60.000 8.29 8.29 46.81 4.85
244 246 1.476891 GATACAGACGACCTGCTGGAA 59.523 52.381 17.64 0.00 46.81 3.53
253 255 0.034089 ACCTGCTGGAATGGGTAAGC 60.034 55.000 17.64 0.00 37.04 3.09
272 275 3.011949 GCGTCTTGCCTGAATCAAAAA 57.988 42.857 0.00 0.00 37.76 1.94
295 298 8.826293 AAAAGCTCAGGATAAGTAGTAGTAGT 57.174 34.615 0.00 0.00 0.00 2.73
298 301 9.509956 AAGCTCAGGATAAGTAGTAGTAGTATG 57.490 37.037 0.00 0.00 0.00 2.39
301 310 9.999660 CTCAGGATAAGTAGTAGTAGTATGACA 57.000 37.037 0.00 0.00 0.00 3.58
396 486 2.111999 CTGGTGGACCCGAAGCTGAA 62.112 60.000 0.00 0.00 35.15 3.02
586 680 0.326264 AGATGTCCCTTGCTTCGCTT 59.674 50.000 0.00 0.00 0.00 4.68
592 686 0.603707 CCCTTGCTTCGCTTCTGTCA 60.604 55.000 0.00 0.00 0.00 3.58
603 721 1.334419 GCTTCTGTCATGTGTGTGTGC 60.334 52.381 0.00 0.00 0.00 4.57
647 773 3.482472 GCTGTCGTGTGTTCATATAGACG 59.518 47.826 0.00 0.00 34.22 4.18
651 777 3.119424 TCGTGTGTTCATATAGACGGCAA 60.119 43.478 0.00 0.00 33.83 4.52
662 788 1.887242 GACGGCAACTGCACAGTGA 60.887 57.895 4.15 0.00 41.58 3.41
679 805 7.384660 TGCACAGTGAATTAATTTGCCTAAAAG 59.615 33.333 15.67 0.00 0.00 2.27
736 863 4.259734 GCGTTAGCATTTTACGAATGTGTG 59.740 41.667 0.00 0.00 44.35 3.82
737 864 5.613812 CGTTAGCATTTTACGAATGTGTGA 58.386 37.500 0.00 0.00 37.47 3.58
740 915 5.034554 AGCATTTTACGAATGTGTGAGTG 57.965 39.130 0.00 0.00 0.00 3.51
747 922 0.239347 GAATGTGTGAGTGTGCTGGC 59.761 55.000 0.00 0.00 0.00 4.85
755 930 2.282040 GTGTGCTGGCTCAGGCTT 60.282 61.111 0.00 0.00 38.73 4.35
756 931 1.900498 GTGTGCTGGCTCAGGCTTT 60.900 57.895 0.00 0.00 38.73 3.51
757 932 1.152694 TGTGCTGGCTCAGGCTTTT 60.153 52.632 0.00 0.00 38.73 2.27
773 948 3.492011 GGCTTTTGTTTTGATGTGCTCAG 59.508 43.478 0.00 0.00 34.68 3.35
812 1003 5.290493 TGAAAGGCTTGTTTGAGTAGAGA 57.710 39.130 0.00 0.00 0.00 3.10
868 1059 2.957474 GCCCATAGAAAAAGGCCCATA 58.043 47.619 0.00 0.00 39.60 2.74
892 1083 3.419732 ACCCAATAAAATCAGGCCCAT 57.580 42.857 0.00 0.00 0.00 4.00
916 1107 2.747989 GAGAAAATCAACGGAAGACCCC 59.252 50.000 0.00 0.00 0.00 4.95
956 1147 4.432712 AGAAACACAAGGCAATTTCACAC 58.567 39.130 0.00 0.00 34.22 3.82
961 1153 3.486841 CACAAGGCAATTTCACACTTTCG 59.513 43.478 0.00 0.00 0.00 3.46
973 1166 1.807742 ACACTTTCGTCGGAGAGAGAG 59.192 52.381 5.81 2.26 36.95 3.20
1134 1329 2.125912 CTCAACCAGCCGTCCTCG 60.126 66.667 0.00 0.00 0.00 4.63
1197 1401 1.065764 CGACGATGCGGATGAGGAA 59.934 57.895 0.00 0.00 0.00 3.36
1275 1482 0.959553 TCAGTGACCAAGACTCCGAC 59.040 55.000 0.00 0.00 0.00 4.79
1288 1495 1.585006 TCCGACGAGGAGTTCAAGC 59.415 57.895 0.00 0.00 45.98 4.01
1319 1526 0.854218 TCTAACCAAAAGGTGCCCCA 59.146 50.000 0.00 0.00 0.00 4.96
1384 1594 2.002586 GTGTGCATCATCGCTGTTAGT 58.997 47.619 0.00 0.00 0.00 2.24
1418 1628 4.094294 TGACGCTATTGTTTTGGTGATAGC 59.906 41.667 4.56 4.56 42.07 2.97
1494 1706 5.387113 TCATGGCATCCTTACAGGTTAAT 57.613 39.130 0.00 0.00 36.53 1.40
1505 1717 7.981142 TCCTTACAGGTTAATTTGCTAAATCG 58.019 34.615 0.00 0.00 36.53 3.34
1510 1722 4.033019 GGTTAATTTGCTAAATCGCGGTC 58.967 43.478 6.13 0.00 0.00 4.79
1522 1735 2.433868 TCGCGGTCTTAGCAATATCC 57.566 50.000 6.13 0.00 34.19 2.59
1596 1809 5.852827 TCCCAAAGAAATGGAATGTGAAAC 58.147 37.500 0.00 0.00 43.54 2.78
1603 1816 5.186409 AGAAATGGAATGTGAAACTCCATGG 59.814 40.000 4.97 4.97 40.64 3.66
1604 1817 3.805066 TGGAATGTGAAACTCCATGGA 57.195 42.857 15.27 15.27 38.04 3.41
1605 1818 3.689347 TGGAATGTGAAACTCCATGGAG 58.311 45.455 35.55 35.55 46.91 3.86
1668 1894 4.392940 TCTCTGCTTTCTTTTCAGGGAAG 58.607 43.478 0.00 0.00 34.67 3.46
1711 1937 6.043358 ACTTGGGAAGCTCTTCTAAAAGTACT 59.957 38.462 16.09 0.00 39.45 2.73
1796 2022 4.210537 AGGTAATACATACGTCGCAAATGC 59.789 41.667 0.00 0.00 35.19 3.56
1850 2078 5.882557 TGCTTATTGAACTCCTGATCCTTTC 59.117 40.000 0.00 0.00 0.00 2.62
1917 2145 4.023291 TGGCAGAACCTTCAAAAAGTTCT 58.977 39.130 0.00 0.00 40.22 3.01
1953 2181 4.095932 ACAGAACCTTCAAAAAGTTCCGTC 59.904 41.667 0.00 0.00 0.00 4.79
2125 2353 8.322828 TGTACAGTATTAGCTTTACATCCCAAA 58.677 33.333 0.00 0.00 29.75 3.28
2283 2511 3.254657 TGGCATTTAAAACCTGAGTTCCG 59.745 43.478 10.89 0.00 34.19 4.30
2313 2541 7.837202 AAATGGATTTTGTGTTGCATCTATG 57.163 32.000 0.00 0.00 0.00 2.23
2351 2579 9.589111 GTTGAGGAAATAGTCTTAGTAGGAAAG 57.411 37.037 0.00 0.00 0.00 2.62
2415 2643 5.331902 CCTTGTGATTTGCGTATTGGTTAG 58.668 41.667 0.00 0.00 0.00 2.34
2486 2714 9.327628 GATTAGTTCTTAAACAGTAATCCCTCC 57.672 37.037 8.65 0.00 37.88 4.30
2487 2715 5.731591 AGTTCTTAAACAGTAATCCCTCCG 58.268 41.667 0.00 0.00 37.88 4.63
2488 2716 5.247792 AGTTCTTAAACAGTAATCCCTCCGT 59.752 40.000 0.00 0.00 37.88 4.69
2489 2717 5.334724 TCTTAAACAGTAATCCCTCCGTC 57.665 43.478 0.00 0.00 0.00 4.79
2490 2718 4.161001 TCTTAAACAGTAATCCCTCCGTCC 59.839 45.833 0.00 0.00 0.00 4.79
2491 2719 1.201424 AACAGTAATCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
2492 2720 0.042131 ACAGTAATCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
2493 2721 1.200519 CAGTAATCCCTCCGTCCCAA 58.799 55.000 0.00 0.00 0.00 4.12
2494 2722 1.557832 CAGTAATCCCTCCGTCCCAAA 59.442 52.381 0.00 0.00 0.00 3.28
2495 2723 2.026636 CAGTAATCCCTCCGTCCCAAAA 60.027 50.000 0.00 0.00 0.00 2.44
2496 2724 2.850568 AGTAATCCCTCCGTCCCAAAAT 59.149 45.455 0.00 0.00 0.00 1.82
2497 2725 2.919772 AATCCCTCCGTCCCAAAATT 57.080 45.000 0.00 0.00 0.00 1.82
2498 2726 2.437085 ATCCCTCCGTCCCAAAATTC 57.563 50.000 0.00 0.00 0.00 2.17
2499 2727 1.368374 TCCCTCCGTCCCAAAATTCT 58.632 50.000 0.00 0.00 0.00 2.40
2500 2728 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2501 2729 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2502 2730 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2503 2731 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2504 2732 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2505 2733 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2506 2734 3.568007 TCCGTCCCAAAATTCTTGTCTTG 59.432 43.478 0.00 0.00 0.00 3.02
2507 2735 3.305335 CCGTCCCAAAATTCTTGTCTTGG 60.305 47.826 0.00 0.00 38.45 3.61
2508 2736 3.568007 CGTCCCAAAATTCTTGTCTTGGA 59.432 43.478 5.99 0.95 40.72 3.53
2509 2737 4.218417 CGTCCCAAAATTCTTGTCTTGGAT 59.782 41.667 5.99 0.00 40.72 3.41
2510 2738 5.278957 CGTCCCAAAATTCTTGTCTTGGATT 60.279 40.000 5.99 0.00 40.72 3.01
2511 2739 6.524734 GTCCCAAAATTCTTGTCTTGGATTT 58.475 36.000 5.99 0.00 40.72 2.17
2512 2740 6.424812 GTCCCAAAATTCTTGTCTTGGATTTG 59.575 38.462 5.99 0.00 40.72 2.32
2513 2741 6.099557 TCCCAAAATTCTTGTCTTGGATTTGT 59.900 34.615 5.99 0.00 40.72 2.83
2514 2742 6.424812 CCCAAAATTCTTGTCTTGGATTTGTC 59.575 38.462 5.99 0.00 40.72 3.18
2515 2743 7.212274 CCAAAATTCTTGTCTTGGATTTGTCT 58.788 34.615 0.00 0.00 40.72 3.41
2516 2744 8.359642 CCAAAATTCTTGTCTTGGATTTGTCTA 58.640 33.333 0.00 0.00 40.72 2.59
2517 2745 9.403110 CAAAATTCTTGTCTTGGATTTGTCTAG 57.597 33.333 0.00 0.00 0.00 2.43
2518 2746 8.924511 AAATTCTTGTCTTGGATTTGTCTAGA 57.075 30.769 0.00 0.00 0.00 2.43
2519 2747 9.525826 AAATTCTTGTCTTGGATTTGTCTAGAT 57.474 29.630 0.00 0.00 0.00 1.98
2522 2750 9.605275 TTCTTGTCTTGGATTTGTCTAGATATG 57.395 33.333 0.00 0.00 0.00 1.78
2523 2751 8.206867 TCTTGTCTTGGATTTGTCTAGATATGG 58.793 37.037 0.00 0.00 0.00 2.74
2524 2752 7.675161 TGTCTTGGATTTGTCTAGATATGGA 57.325 36.000 0.00 0.00 0.00 3.41
2525 2753 8.267620 TGTCTTGGATTTGTCTAGATATGGAT 57.732 34.615 0.00 0.00 0.00 3.41
2526 2754 8.152898 TGTCTTGGATTTGTCTAGATATGGATG 58.847 37.037 0.00 0.00 0.00 3.51
2527 2755 8.153550 GTCTTGGATTTGTCTAGATATGGATGT 58.846 37.037 0.00 0.00 0.00 3.06
2528 2756 9.379770 TCTTGGATTTGTCTAGATATGGATGTA 57.620 33.333 0.00 0.00 0.00 2.29
2529 2757 9.429359 CTTGGATTTGTCTAGATATGGATGTAC 57.571 37.037 0.00 0.00 0.00 2.90
2530 2758 7.907389 TGGATTTGTCTAGATATGGATGTACC 58.093 38.462 0.00 0.00 39.54 3.34
2531 2759 7.734865 TGGATTTGTCTAGATATGGATGTACCT 59.265 37.037 0.00 0.00 39.86 3.08
2532 2760 9.256228 GGATTTGTCTAGATATGGATGTACCTA 57.744 37.037 0.00 0.00 39.86 3.08
2547 2775 9.826574 TGGATGTACCTAATACTAAAACATGAC 57.173 33.333 0.00 0.00 39.86 3.06
2559 2787 7.539712 ACTAAAACATGACTTGATACATCCG 57.460 36.000 0.00 0.00 0.00 4.18
2560 2788 7.103641 ACTAAAACATGACTTGATACATCCGT 58.896 34.615 0.00 0.00 0.00 4.69
2561 2789 6.817765 AAAACATGACTTGATACATCCGTT 57.182 33.333 0.00 0.00 0.00 4.44
2562 2790 6.817765 AAACATGACTTGATACATCCGTTT 57.182 33.333 0.00 0.00 0.00 3.60
2563 2791 6.817765 AACATGACTTGATACATCCGTTTT 57.182 33.333 0.00 0.00 0.00 2.43
2564 2792 6.817765 ACATGACTTGATACATCCGTTTTT 57.182 33.333 0.00 0.00 0.00 1.94
2565 2793 7.915293 ACATGACTTGATACATCCGTTTTTA 57.085 32.000 0.00 0.00 0.00 1.52
2566 2794 7.974675 ACATGACTTGATACATCCGTTTTTAG 58.025 34.615 0.00 0.00 0.00 1.85
2567 2795 7.822334 ACATGACTTGATACATCCGTTTTTAGA 59.178 33.333 0.00 0.00 0.00 2.10
2568 2796 7.591006 TGACTTGATACATCCGTTTTTAGAC 57.409 36.000 0.00 0.00 0.00 2.59
2569 2797 7.156000 TGACTTGATACATCCGTTTTTAGACA 58.844 34.615 0.00 0.00 0.00 3.41
2570 2798 7.658167 TGACTTGATACATCCGTTTTTAGACAA 59.342 33.333 0.00 0.00 0.00 3.18
2571 2799 8.385898 ACTTGATACATCCGTTTTTAGACAAA 57.614 30.769 0.00 0.00 0.00 2.83
2572 2800 9.010029 ACTTGATACATCCGTTTTTAGACAAAT 57.990 29.630 0.00 0.00 0.00 2.32
2573 2801 9.490663 CTTGATACATCCGTTTTTAGACAAATC 57.509 33.333 0.00 0.00 0.00 2.17
2574 2802 8.786826 TGATACATCCGTTTTTAGACAAATCT 57.213 30.769 0.00 0.00 39.15 2.40
2575 2803 9.878667 TGATACATCCGTTTTTAGACAAATCTA 57.121 29.630 0.00 0.00 36.29 1.98
2578 2806 8.842358 ACATCCGTTTTTAGACAAATCTAAGA 57.158 30.769 0.00 0.00 45.93 2.10
2579 2807 8.718734 ACATCCGTTTTTAGACAAATCTAAGAC 58.281 33.333 0.00 1.47 45.93 3.01
2580 2808 8.717821 CATCCGTTTTTAGACAAATCTAAGACA 58.282 33.333 10.58 0.00 45.93 3.41
2581 2809 8.665643 TCCGTTTTTAGACAAATCTAAGACAA 57.334 30.769 10.58 0.00 45.93 3.18
2582 2810 8.770828 TCCGTTTTTAGACAAATCTAAGACAAG 58.229 33.333 10.58 4.79 45.93 3.16
2583 2811 8.770828 CCGTTTTTAGACAAATCTAAGACAAGA 58.229 33.333 10.58 0.00 45.93 3.02
2591 2819 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2592 2820 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2593 2821 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2594 2822 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2595 2823 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2596 2824 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2597 2825 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2598 2826 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2599 2827 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2792 3020 9.088987 ACTTTTATATGGACTGTGAATTGGTTT 57.911 29.630 0.00 0.00 0.00 3.27
2801 3029 6.262273 GGACTGTGAATTGGTTTCTACTTTGA 59.738 38.462 0.00 0.00 35.23 2.69
2834 3062 2.026729 TGGAAAAGGATACATCGCACCA 60.027 45.455 0.00 0.00 41.41 4.17
2915 3143 6.932356 TCTAAGATGATCCATTGCTTTGAC 57.068 37.500 0.00 0.00 0.00 3.18
3059 3287 1.352017 TCTGTGCACTCATGGAACCAT 59.648 47.619 19.41 0.00 37.08 3.55
3062 3290 3.949754 CTGTGCACTCATGGAACCATATT 59.050 43.478 19.41 0.00 34.91 1.28
3078 3306 9.019764 GGAACCATATTCAAATCAATTAACACG 57.980 33.333 0.00 0.00 0.00 4.49
3098 3334 1.318576 GACAACTGGTTCCCTTGTGG 58.681 55.000 6.70 0.00 0.00 4.17
3162 3398 2.564721 GCCTGTTTTCGCCAAGCCT 61.565 57.895 0.00 0.00 0.00 4.58
3165 3401 0.239347 CTGTTTTCGCCAAGCCTGAG 59.761 55.000 0.00 0.00 0.00 3.35
3180 3416 2.486907 GCCTGAGCTAGCAGATTTCCAT 60.487 50.000 18.83 0.00 38.14 3.41
3185 3421 4.820173 TGAGCTAGCAGATTTCCATCATTG 59.180 41.667 18.83 0.00 0.00 2.82
3209 3445 4.101430 CCCCTGCTATTTGCCAATGTATTT 59.899 41.667 0.00 0.00 42.00 1.40
3224 3460 9.369904 GCCAATGTATTTAAGAATGTGAATTGT 57.630 29.630 0.00 0.00 0.00 2.71
3271 3507 8.901472 TGACTAGCAATTATATACTCCATCCT 57.099 34.615 0.00 0.00 0.00 3.24
3272 3508 9.326489 TGACTAGCAATTATATACTCCATCCTT 57.674 33.333 0.00 0.00 0.00 3.36
3284 3520 2.797156 CTCCATCCTTTTGATAGTCGCG 59.203 50.000 0.00 0.00 30.56 5.87
3285 3521 2.167693 TCCATCCTTTTGATAGTCGCGT 59.832 45.455 5.77 0.00 30.56 6.01
3287 3523 2.288961 TCCTTTTGATAGTCGCGTCC 57.711 50.000 5.77 0.00 0.00 4.79
3289 3525 3.018856 TCCTTTTGATAGTCGCGTCCTA 58.981 45.455 5.77 8.40 0.00 2.94
3610 3851 4.430007 CAGCGCTACAATAAGGAGTGTTA 58.570 43.478 10.99 0.00 35.11 2.41
3612 3853 4.868734 AGCGCTACAATAAGGAGTGTTAAC 59.131 41.667 8.99 0.00 35.11 2.01
3631 3872 7.708752 GTGTTAACCTTTTGAACATGAATCCAA 59.291 33.333 0.00 0.00 35.65 3.53
3715 3956 3.096541 CAACATGTTGCAAGAGCCG 57.903 52.632 24.69 0.00 41.13 5.52
3716 3957 0.387622 CAACATGTTGCAAGAGCCGG 60.388 55.000 24.69 0.00 41.13 6.13
3717 3958 0.537143 AACATGTTGCAAGAGCCGGA 60.537 50.000 11.07 0.00 41.13 5.14
3718 3959 0.957395 ACATGTTGCAAGAGCCGGAG 60.957 55.000 5.05 0.00 41.13 4.63
3719 3960 0.957395 CATGTTGCAAGAGCCGGAGT 60.957 55.000 5.05 0.00 41.13 3.85
3720 3961 0.957395 ATGTTGCAAGAGCCGGAGTG 60.957 55.000 5.05 0.00 41.13 3.51
3721 3962 1.301716 GTTGCAAGAGCCGGAGTGA 60.302 57.895 5.05 0.00 41.13 3.41
3722 3963 0.674895 GTTGCAAGAGCCGGAGTGAT 60.675 55.000 5.05 0.00 41.13 3.06
3723 3964 0.674581 TTGCAAGAGCCGGAGTGATG 60.675 55.000 5.05 0.00 41.13 3.07
3724 3965 1.219124 GCAAGAGCCGGAGTGATGA 59.781 57.895 5.05 0.00 33.58 2.92
3725 3966 0.179062 GCAAGAGCCGGAGTGATGAT 60.179 55.000 5.05 0.00 33.58 2.45
3726 3967 1.579698 CAAGAGCCGGAGTGATGATG 58.420 55.000 5.05 0.00 0.00 3.07
3727 3968 1.137675 CAAGAGCCGGAGTGATGATGA 59.862 52.381 5.05 0.00 0.00 2.92
3728 3969 0.749649 AGAGCCGGAGTGATGATGAC 59.250 55.000 5.05 0.00 0.00 3.06
3729 3970 0.461548 GAGCCGGAGTGATGATGACA 59.538 55.000 5.05 0.00 0.00 3.58
3730 3971 0.463204 AGCCGGAGTGATGATGACAG 59.537 55.000 5.05 0.00 0.00 3.51
3731 3972 0.531532 GCCGGAGTGATGATGACAGG 60.532 60.000 5.05 0.00 0.00 4.00
3732 3973 0.105593 CCGGAGTGATGATGACAGGG 59.894 60.000 0.00 0.00 0.00 4.45
3733 3974 0.531532 CGGAGTGATGATGACAGGGC 60.532 60.000 0.00 0.00 0.00 5.19
3734 3975 0.543277 GGAGTGATGATGACAGGGCA 59.457 55.000 0.00 0.00 0.00 5.36
3735 3976 1.065199 GGAGTGATGATGACAGGGCAA 60.065 52.381 0.00 0.00 0.00 4.52
3736 3977 2.618816 GGAGTGATGATGACAGGGCAAA 60.619 50.000 0.00 0.00 0.00 3.68
3737 3978 2.421424 GAGTGATGATGACAGGGCAAAC 59.579 50.000 0.00 0.00 0.00 2.93
3738 3979 2.161855 GTGATGATGACAGGGCAAACA 58.838 47.619 0.00 0.00 0.00 2.83
3739 3980 2.163010 GTGATGATGACAGGGCAAACAG 59.837 50.000 0.00 0.00 0.00 3.16
3740 3981 2.224843 TGATGATGACAGGGCAAACAGT 60.225 45.455 0.00 0.00 0.00 3.55
3741 3982 2.363306 TGATGACAGGGCAAACAGTT 57.637 45.000 0.00 0.00 0.00 3.16
3742 3983 1.955778 TGATGACAGGGCAAACAGTTG 59.044 47.619 0.00 0.00 37.83 3.16
3818 4059 4.202326 ACCTAACTATTAAGACGGCATGGG 60.202 45.833 0.00 0.00 0.00 4.00
3836 4077 2.024846 TGGGTTTGAAGGTGAAACTGGA 60.025 45.455 0.00 0.00 36.74 3.86
3877 4118 3.265791 GAGGCATGAGTCGATGAAAGTT 58.734 45.455 0.00 0.00 0.00 2.66
3885 4126 2.028020 AGTCGATGAAAGTTCCAGGACC 60.028 50.000 0.00 0.00 0.00 4.46
3921 4162 3.851458 TCACAGGAGCTGCATATCAAT 57.149 42.857 8.35 0.00 34.37 2.57
3922 4163 3.736720 TCACAGGAGCTGCATATCAATC 58.263 45.455 8.35 0.00 34.37 2.67
3923 4164 3.135167 TCACAGGAGCTGCATATCAATCA 59.865 43.478 8.35 0.00 34.37 2.57
3924 4165 3.881089 CACAGGAGCTGCATATCAATCAA 59.119 43.478 8.35 0.00 34.37 2.57
3925 4166 4.023963 CACAGGAGCTGCATATCAATCAAG 60.024 45.833 8.35 0.00 34.37 3.02
3926 4167 3.502595 CAGGAGCTGCATATCAATCAAGG 59.497 47.826 8.35 0.00 0.00 3.61
3928 4169 3.501445 GGAGCTGCATATCAATCAAGGTC 59.499 47.826 0.00 0.00 0.00 3.85
4049 4309 3.379372 TCGCCGTGCTCTTATTTACTACT 59.621 43.478 0.00 0.00 0.00 2.57
4050 4310 3.486108 CGCCGTGCTCTTATTTACTACTG 59.514 47.826 0.00 0.00 0.00 2.74
4051 4311 3.245519 GCCGTGCTCTTATTTACTACTGC 59.754 47.826 0.00 0.00 0.00 4.40
4052 4312 4.430007 CCGTGCTCTTATTTACTACTGCA 58.570 43.478 0.00 0.00 0.00 4.41
4245 4607 5.981174 AGTTATACTAACGCCCAAGCTAAA 58.019 37.500 0.00 0.00 36.60 1.85
4384 4746 2.559668 TGCTGTTAAGTAGTAGTGCCGT 59.440 45.455 0.00 0.00 0.00 5.68
4461 4823 1.078759 CAGGAGCCTAACAAGACGCG 61.079 60.000 3.53 3.53 0.00 6.01
4605 5025 0.397941 TCTCACAAGGTCCTGCCAAG 59.602 55.000 0.00 0.00 40.61 3.61
4614 5034 0.804989 GTCCTGCCAAGATTCAACGG 59.195 55.000 0.00 0.00 0.00 4.44
4659 5079 0.388134 GGCTTCAACATGCACAGCTG 60.388 55.000 13.48 13.48 0.00 4.24
4660 5080 0.594602 GCTTCAACATGCACAGCTGA 59.405 50.000 23.35 0.00 0.00 4.26
4661 5081 1.001048 GCTTCAACATGCACAGCTGAA 60.001 47.619 23.35 5.79 0.00 3.02
4662 5082 2.544277 GCTTCAACATGCACAGCTGAAA 60.544 45.455 23.35 5.39 0.00 2.69
4663 5083 3.859627 GCTTCAACATGCACAGCTGAAAT 60.860 43.478 23.35 7.73 0.00 2.17
4664 5084 4.304110 CTTCAACATGCACAGCTGAAATT 58.696 39.130 23.35 2.71 0.00 1.82
4665 5085 4.325028 TCAACATGCACAGCTGAAATTT 57.675 36.364 23.35 2.48 0.00 1.82
4666 5086 5.450592 TCAACATGCACAGCTGAAATTTA 57.549 34.783 23.35 0.39 0.00 1.40
4667 5087 5.840715 TCAACATGCACAGCTGAAATTTAA 58.159 33.333 23.35 0.00 0.00 1.52
4668 5088 5.691305 TCAACATGCACAGCTGAAATTTAAC 59.309 36.000 23.35 0.60 0.00 2.01
4669 5089 5.199024 ACATGCACAGCTGAAATTTAACA 57.801 34.783 23.35 6.47 0.00 2.41
4670 5090 5.224888 ACATGCACAGCTGAAATTTAACAG 58.775 37.500 23.35 3.15 37.22 3.16
4697 5117 9.901172 CTTTTCCCATAGTAAACTAGTACCAAT 57.099 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.524569 AACAAAACCCATTTCGGCTG 57.475 45.000 0.00 0.00 0.00 4.85
4 5 3.868077 TCTGCAAAACAAAACCCATTTCG 59.132 39.130 0.00 0.00 0.00 3.46
18 19 6.092670 CCTCTCGAAGTCAATTATCTGCAAAA 59.907 38.462 0.00 0.00 0.00 2.44
142 144 1.745489 GGCCTGGACGTCCATGAAC 60.745 63.158 35.31 24.82 46.46 3.18
226 228 1.204704 CATTCCAGCAGGTCGTCTGTA 59.795 52.381 0.00 0.00 45.08 2.74
239 241 2.009774 CAAGACGCTTACCCATTCCAG 58.990 52.381 0.00 0.00 0.00 3.86
242 244 0.733150 GGCAAGACGCTTACCCATTC 59.267 55.000 0.00 0.00 41.91 2.67
244 246 0.392998 CAGGCAAGACGCTTACCCAT 60.393 55.000 5.54 0.00 41.91 4.00
272 275 9.509956 CATACTACTACTACTTATCCTGAGCTT 57.490 37.037 0.00 0.00 0.00 3.74
274 277 8.938906 GTCATACTACTACTACTTATCCTGAGC 58.061 40.741 0.00 0.00 0.00 4.26
297 300 9.996554 TGATTTAGTTCTCTTGTAGATTTGTCA 57.003 29.630 0.00 0.00 33.05 3.58
326 341 2.935238 GCTTCCTCGCCTGAAACACATA 60.935 50.000 0.00 0.00 0.00 2.29
329 344 0.884704 TGCTTCCTCGCCTGAAACAC 60.885 55.000 0.00 0.00 0.00 3.32
396 486 4.704103 TCTCCTGGCCCACGCTCT 62.704 66.667 0.00 0.00 34.44 4.09
586 680 0.179086 ACGCACACACACATGACAGA 60.179 50.000 0.00 0.00 0.00 3.41
592 686 1.024046 ACACACACGCACACACACAT 61.024 50.000 0.00 0.00 0.00 3.21
603 721 1.298041 GCCCGTCAAAACACACACG 60.298 57.895 0.00 0.00 0.00 4.49
647 773 3.641437 TTAATTCACTGTGCAGTTGCC 57.359 42.857 2.12 0.00 40.20 4.52
651 777 4.281688 AGGCAAATTAATTCACTGTGCAGT 59.718 37.500 18.63 0.00 43.61 4.40
679 805 6.928520 AGACATGGATCAAAAACCAATCTTC 58.071 36.000 0.00 0.00 39.69 2.87
724 851 2.799978 CAGCACACTCACACATTCGTAA 59.200 45.455 0.00 0.00 0.00 3.18
726 853 1.220529 CAGCACACTCACACATTCGT 58.779 50.000 0.00 0.00 0.00 3.85
727 854 0.514255 CCAGCACACTCACACATTCG 59.486 55.000 0.00 0.00 0.00 3.34
729 856 0.179009 AGCCAGCACACTCACACATT 60.179 50.000 0.00 0.00 0.00 2.71
731 858 1.227645 GAGCCAGCACACTCACACA 60.228 57.895 0.00 0.00 32.98 3.72
732 859 1.226686 CTGAGCCAGCACACTCACAC 61.227 60.000 0.00 0.00 37.99 3.82
733 860 1.070275 CTGAGCCAGCACACTCACA 59.930 57.895 0.00 0.00 37.99 3.58
736 863 2.744768 AAGCCTGAGCCAGCACACTC 62.745 60.000 0.00 0.00 41.25 3.51
737 864 2.349100 AAAGCCTGAGCCAGCACACT 62.349 55.000 0.00 0.00 41.25 3.55
740 915 1.288127 CAAAAGCCTGAGCCAGCAC 59.712 57.895 0.00 0.00 41.25 4.40
747 922 3.492011 GCACATCAAAACAAAAGCCTGAG 59.508 43.478 0.00 0.00 0.00 3.35
790 981 5.290493 TCTCTACTCAAACAAGCCTTTCA 57.710 39.130 0.00 0.00 0.00 2.69
812 1003 1.912043 GGATGGGCTGTAGGCAGATAT 59.088 52.381 7.77 0.00 45.28 1.63
860 1051 4.551215 TTTATTGGGTTGATATGGGCCT 57.449 40.909 4.53 0.00 0.00 5.19
868 1059 3.711190 GGGCCTGATTTTATTGGGTTGAT 59.289 43.478 0.84 0.00 0.00 2.57
892 1083 4.240096 GGTCTTCCGTTGATTTTCTCGTA 58.760 43.478 0.00 0.00 0.00 3.43
956 1147 1.740297 TCCTCTCTCTCCGACGAAAG 58.260 55.000 0.00 0.00 0.00 2.62
1230 1434 4.179599 CCCTCCTCCTCCTCCCCC 62.180 77.778 0.00 0.00 0.00 5.40
1232 1436 3.767044 GAGCCCTCCTCCTCCTCCC 62.767 73.684 0.00 0.00 34.35 4.30
1256 1463 0.959553 GTCGGAGTCTTGGTCACTGA 59.040 55.000 0.00 0.00 0.00 3.41
1275 1482 0.610687 AGGAAGGCTTGAACTCCTCG 59.389 55.000 3.46 0.00 0.00 4.63
1288 1495 5.338463 CCTTTTGGTTAGACCTAGAGGAAGG 60.338 48.000 11.05 4.51 44.33 3.46
1319 1526 4.265904 GGATTTGTTCCACCGGAAAATT 57.734 40.909 9.46 0.00 43.86 1.82
1384 1594 9.767684 CAAAACAATAGCGTCAACTAATTCATA 57.232 29.630 0.00 0.00 0.00 2.15
1441 1651 4.889409 CACTAACCCTGATGGCATTACAAT 59.111 41.667 0.00 0.00 37.83 2.71
1454 1664 1.202879 TGAACAAGCCCACTAACCCTG 60.203 52.381 0.00 0.00 0.00 4.45
1494 1706 2.350498 GCTAAGACCGCGATTTAGCAAA 59.650 45.455 28.18 2.26 45.30 3.68
1505 1717 2.224314 GCTTGGATATTGCTAAGACCGC 59.776 50.000 0.00 0.00 0.00 5.68
1510 1722 4.096833 TGTTGCTGCTTGGATATTGCTAAG 59.903 41.667 0.00 0.00 0.00 2.18
1596 1809 3.842007 AAAGAGCAGATCTCCATGGAG 57.158 47.619 32.60 32.60 42.90 3.86
1668 1894 4.751600 CCAAGTTCATTTTCTTCTTTGCCC 59.248 41.667 0.00 0.00 0.00 5.36
1711 1937 4.021016 GGAGCACCTTCTTCTTCTCTAACA 60.021 45.833 0.00 0.00 0.00 2.41
1796 2022 1.444212 CATCCGTTTTTGGCGCCTG 60.444 57.895 29.70 10.32 0.00 4.85
1850 2078 2.208431 GGCGAAGAATCATGAGTGGAG 58.792 52.381 0.00 0.00 0.00 3.86
1917 2145 2.004017 GGTTCTGTTGTTGTCGTCACA 58.996 47.619 0.00 0.00 0.00 3.58
2082 2310 5.089970 TGTACATGTCATTCTGGAAGGAG 57.910 43.478 0.00 0.00 31.29 3.69
2125 2353 7.042791 GCACAATTATGCAAAACACAAGTAAGT 60.043 33.333 3.24 0.00 45.39 2.24
2283 2511 5.695816 TGCAACACAAAATCCATTTTCTAGC 59.304 36.000 0.00 0.00 37.86 3.42
2313 2541 8.986477 ACTATTTCCTCAACAAACAATTATGC 57.014 30.769 0.00 0.00 0.00 3.14
2351 2579 6.166982 CCTATGTTACTTTAGGCTCATAGGC 58.833 44.000 17.94 0.00 43.87 3.93
2415 2643 4.360563 CAGGATCACACCATACGTAACTC 58.639 47.826 0.00 0.00 0.00 3.01
2475 2703 1.961133 TTTGGGACGGAGGGATTACT 58.039 50.000 0.00 0.00 0.00 2.24
2476 2704 2.793288 TTTTGGGACGGAGGGATTAC 57.207 50.000 0.00 0.00 0.00 1.89
2477 2705 3.526019 AGAATTTTGGGACGGAGGGATTA 59.474 43.478 0.00 0.00 0.00 1.75
2478 2706 2.311841 AGAATTTTGGGACGGAGGGATT 59.688 45.455 0.00 0.00 0.00 3.01
2479 2707 1.923148 AGAATTTTGGGACGGAGGGAT 59.077 47.619 0.00 0.00 0.00 3.85
2480 2708 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2481 2709 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2482 2710 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2483 2711 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2484 2712 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2485 2713 3.305335 CCAAGACAAGAATTTTGGGACGG 60.305 47.826 0.00 0.00 37.11 4.79
2486 2714 3.568007 TCCAAGACAAGAATTTTGGGACG 59.432 43.478 4.84 0.00 40.33 4.79
2487 2715 5.728637 ATCCAAGACAAGAATTTTGGGAC 57.271 39.130 4.84 0.00 40.33 4.46
2488 2716 6.099557 ACAAATCCAAGACAAGAATTTTGGGA 59.900 34.615 4.84 0.00 40.33 4.37
2489 2717 6.290605 ACAAATCCAAGACAAGAATTTTGGG 58.709 36.000 4.84 0.00 40.33 4.12
2490 2718 7.212274 AGACAAATCCAAGACAAGAATTTTGG 58.788 34.615 0.00 0.00 41.09 3.28
2491 2719 9.403110 CTAGACAAATCCAAGACAAGAATTTTG 57.597 33.333 0.00 0.00 0.00 2.44
2492 2720 9.354673 TCTAGACAAATCCAAGACAAGAATTTT 57.645 29.630 0.00 0.00 0.00 1.82
2493 2721 8.924511 TCTAGACAAATCCAAGACAAGAATTT 57.075 30.769 0.00 0.00 0.00 1.82
2496 2724 9.605275 CATATCTAGACAAATCCAAGACAAGAA 57.395 33.333 0.00 0.00 0.00 2.52
2497 2725 8.206867 CCATATCTAGACAAATCCAAGACAAGA 58.793 37.037 0.00 0.00 0.00 3.02
2498 2726 8.206867 TCCATATCTAGACAAATCCAAGACAAG 58.793 37.037 0.00 0.00 0.00 3.16
2499 2727 8.089625 TCCATATCTAGACAAATCCAAGACAA 57.910 34.615 0.00 0.00 0.00 3.18
2500 2728 7.675161 TCCATATCTAGACAAATCCAAGACA 57.325 36.000 0.00 0.00 0.00 3.41
2501 2729 8.153550 ACATCCATATCTAGACAAATCCAAGAC 58.846 37.037 0.00 0.00 0.00 3.01
2502 2730 8.267620 ACATCCATATCTAGACAAATCCAAGA 57.732 34.615 0.00 0.00 0.00 3.02
2503 2731 9.429359 GTACATCCATATCTAGACAAATCCAAG 57.571 37.037 0.00 0.00 0.00 3.61
2504 2732 8.375506 GGTACATCCATATCTAGACAAATCCAA 58.624 37.037 0.00 0.00 35.97 3.53
2505 2733 7.734865 AGGTACATCCATATCTAGACAAATCCA 59.265 37.037 0.00 0.00 39.02 3.41
2506 2734 8.140112 AGGTACATCCATATCTAGACAAATCC 57.860 38.462 0.00 0.00 39.02 3.01
2521 2749 9.826574 GTCATGTTTTAGTATTAGGTACATCCA 57.173 33.333 0.00 0.00 39.02 3.41
2533 2761 9.261180 CGGATGTATCAAGTCATGTTTTAGTAT 57.739 33.333 0.00 0.00 0.00 2.12
2534 2762 8.255206 ACGGATGTATCAAGTCATGTTTTAGTA 58.745 33.333 0.00 0.00 0.00 1.82
2535 2763 7.103641 ACGGATGTATCAAGTCATGTTTTAGT 58.896 34.615 0.00 0.00 0.00 2.24
2536 2764 7.539712 ACGGATGTATCAAGTCATGTTTTAG 57.460 36.000 0.00 0.00 0.00 1.85
2537 2765 7.915293 AACGGATGTATCAAGTCATGTTTTA 57.085 32.000 0.00 0.00 0.00 1.52
2538 2766 6.817765 AACGGATGTATCAAGTCATGTTTT 57.182 33.333 0.00 0.00 0.00 2.43
2539 2767 6.817765 AAACGGATGTATCAAGTCATGTTT 57.182 33.333 0.00 0.00 0.00 2.83
2540 2768 6.817765 AAAACGGATGTATCAAGTCATGTT 57.182 33.333 0.00 0.00 0.00 2.71
2541 2769 6.817765 AAAAACGGATGTATCAAGTCATGT 57.182 33.333 0.00 0.00 0.00 3.21
2542 2770 8.116753 GTCTAAAAACGGATGTATCAAGTCATG 58.883 37.037 0.00 0.00 0.00 3.07
2543 2771 7.822334 TGTCTAAAAACGGATGTATCAAGTCAT 59.178 33.333 0.00 0.00 0.00 3.06
2544 2772 7.156000 TGTCTAAAAACGGATGTATCAAGTCA 58.844 34.615 0.00 0.00 0.00 3.41
2545 2773 7.591006 TGTCTAAAAACGGATGTATCAAGTC 57.409 36.000 0.00 0.00 0.00 3.01
2546 2774 7.972832 TTGTCTAAAAACGGATGTATCAAGT 57.027 32.000 0.00 0.00 0.00 3.16
2547 2775 9.490663 GATTTGTCTAAAAACGGATGTATCAAG 57.509 33.333 0.00 0.00 0.00 3.02
2548 2776 9.226606 AGATTTGTCTAAAAACGGATGTATCAA 57.773 29.630 0.00 0.00 0.00 2.57
2549 2777 8.786826 AGATTTGTCTAAAAACGGATGTATCA 57.213 30.769 0.00 0.00 0.00 2.15
2552 2780 9.932207 TCTTAGATTTGTCTAAAAACGGATGTA 57.068 29.630 0.26 0.00 32.51 2.29
2553 2781 8.718734 GTCTTAGATTTGTCTAAAAACGGATGT 58.281 33.333 0.26 0.00 32.51 3.06
2554 2782 8.717821 TGTCTTAGATTTGTCTAAAAACGGATG 58.282 33.333 0.26 0.00 32.51 3.51
2555 2783 8.842358 TGTCTTAGATTTGTCTAAAAACGGAT 57.158 30.769 0.26 0.00 32.51 4.18
2556 2784 8.665643 TTGTCTTAGATTTGTCTAAAAACGGA 57.334 30.769 0.26 0.00 32.51 4.69
2557 2785 8.770828 TCTTGTCTTAGATTTGTCTAAAAACGG 58.229 33.333 0.26 1.01 32.51 4.44
2565 2793 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2566 2794 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2567 2795 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2568 2796 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2569 2797 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2570 2798 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2571 2799 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2572 2800 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2573 2801 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2574 2802 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2575 2803 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2576 2804 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2577 2805 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2578 2806 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2579 2807 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2580 2808 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2581 2809 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2582 2810 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2583 2811 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2584 2812 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2585 2813 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2586 2814 1.835531 GAATACTCCCTCCGTCCCAAA 59.164 52.381 0.00 0.00 0.00 3.28
2587 2815 1.273381 TGAATACTCCCTCCGTCCCAA 60.273 52.381 0.00 0.00 0.00 4.12
2588 2816 0.337082 TGAATACTCCCTCCGTCCCA 59.663 55.000 0.00 0.00 0.00 4.37
2589 2817 1.138464 GTTGAATACTCCCTCCGTCCC 59.862 57.143 0.00 0.00 0.00 4.46
2590 2818 1.829222 TGTTGAATACTCCCTCCGTCC 59.171 52.381 0.00 0.00 0.00 4.79
2591 2819 3.522553 CTTGTTGAATACTCCCTCCGTC 58.477 50.000 0.00 0.00 0.00 4.79
2592 2820 2.354805 GCTTGTTGAATACTCCCTCCGT 60.355 50.000 0.00 0.00 0.00 4.69
2593 2821 2.280628 GCTTGTTGAATACTCCCTCCG 58.719 52.381 0.00 0.00 0.00 4.63
2594 2822 2.026262 TGGCTTGTTGAATACTCCCTCC 60.026 50.000 0.00 0.00 0.00 4.30
2595 2823 3.350219 TGGCTTGTTGAATACTCCCTC 57.650 47.619 0.00 0.00 0.00 4.30
2596 2824 3.690460 CTTGGCTTGTTGAATACTCCCT 58.310 45.455 0.00 0.00 0.00 4.20
2597 2825 2.164422 GCTTGGCTTGTTGAATACTCCC 59.836 50.000 0.00 0.00 0.00 4.30
2598 2826 3.084786 AGCTTGGCTTGTTGAATACTCC 58.915 45.455 0.00 0.00 33.89 3.85
2599 2827 3.753272 TCAGCTTGGCTTGTTGAATACTC 59.247 43.478 0.00 0.00 36.40 2.59
2766 2994 8.650143 AACCAATTCACAGTCCATATAAAAGT 57.350 30.769 0.00 0.00 0.00 2.66
2767 2995 9.573133 GAAACCAATTCACAGTCCATATAAAAG 57.427 33.333 0.00 0.00 37.99 2.27
2768 2996 9.308000 AGAAACCAATTCACAGTCCATATAAAA 57.692 29.630 0.00 0.00 40.72 1.52
2769 2997 8.877864 AGAAACCAATTCACAGTCCATATAAA 57.122 30.769 0.00 0.00 40.72 1.40
2772 3000 7.633789 AGTAGAAACCAATTCACAGTCCATAT 58.366 34.615 0.00 0.00 40.72 1.78
2792 3020 5.480422 TCCAGCTTCTGTACATCAAAGTAGA 59.520 40.000 0.00 0.00 0.00 2.59
2801 3029 4.640771 TCCTTTTCCAGCTTCTGTACAT 57.359 40.909 0.00 0.00 0.00 2.29
2915 3143 5.163519 ACAAACCTTTCCATCTTTGTCACTG 60.164 40.000 0.00 0.00 32.59 3.66
3014 3242 7.881775 AATCAGACTATTTATGGTTTCCCAC 57.118 36.000 0.00 0.00 45.65 4.61
3023 3251 8.206325 AGTGCACAGAAATCAGACTATTTATG 57.794 34.615 21.04 0.00 41.56 1.90
3028 3256 5.411831 TGAGTGCACAGAAATCAGACTAT 57.588 39.130 21.04 0.00 0.00 2.12
3040 3268 1.830279 ATGGTTCCATGAGTGCACAG 58.170 50.000 21.04 5.63 0.00 3.66
3059 3287 8.788806 AGTTGTCCGTGTTAATTGATTTGAATA 58.211 29.630 0.00 0.00 0.00 1.75
3062 3290 6.434596 CAGTTGTCCGTGTTAATTGATTTGA 58.565 36.000 0.00 0.00 0.00 2.69
3122 3358 4.012374 CACCACCTGAGAAGTGCATTTAT 58.988 43.478 0.00 0.00 33.75 1.40
3123 3359 3.411446 CACCACCTGAGAAGTGCATTTA 58.589 45.455 0.00 0.00 33.75 1.40
3162 3398 4.701651 ATGATGGAAATCTGCTAGCTCA 57.298 40.909 17.23 8.10 0.00 4.26
3165 3401 3.305199 GGCAATGATGGAAATCTGCTAGC 60.305 47.826 8.10 8.10 0.00 3.42
3180 3416 1.113788 GCAAATAGCAGGGGCAATGA 58.886 50.000 0.00 0.00 44.61 2.57
3230 3466 6.859017 TGCTAGTCAATAAGTACACGATGAA 58.141 36.000 0.00 0.00 0.00 2.57
3233 3469 9.982651 ATAATTGCTAGTCAATAAGTACACGAT 57.017 29.630 11.24 0.00 44.23 3.73
3263 3499 2.797156 CGCGACTATCAAAAGGATGGAG 59.203 50.000 0.00 0.00 37.86 3.86
3264 3500 2.167693 ACGCGACTATCAAAAGGATGGA 59.832 45.455 15.93 0.00 37.86 3.41
3266 3502 2.540101 GGACGCGACTATCAAAAGGATG 59.460 50.000 15.93 0.00 36.72 3.51
3267 3503 2.431057 AGGACGCGACTATCAAAAGGAT 59.569 45.455 15.93 0.00 40.14 3.24
3268 3504 1.822990 AGGACGCGACTATCAAAAGGA 59.177 47.619 15.93 0.00 0.00 3.36
3269 3505 2.295253 AGGACGCGACTATCAAAAGG 57.705 50.000 15.93 0.00 0.00 3.11
3270 3506 4.030134 AGTAGGACGCGACTATCAAAAG 57.970 45.455 15.93 0.00 0.00 2.27
3271 3507 4.445452 AAGTAGGACGCGACTATCAAAA 57.555 40.909 15.93 0.00 0.00 2.44
3272 3508 4.445452 AAAGTAGGACGCGACTATCAAA 57.555 40.909 15.93 0.00 0.00 2.69
3274 3510 4.445452 AAAAAGTAGGACGCGACTATCA 57.555 40.909 15.93 0.00 0.00 2.15
3315 3551 5.888691 TCAGTAGTGCAAGTTGACAAAAA 57.111 34.783 7.16 0.00 0.00 1.94
3610 3851 7.738847 AGAATTGGATTCATGTTCAAAAGGTT 58.261 30.769 3.76 0.00 41.71 3.50
3612 3853 9.143631 GTAAGAATTGGATTCATGTTCAAAAGG 57.856 33.333 3.76 0.00 41.71 3.11
3631 3872 8.912988 TGTGAAGGAAAATTGAGTTGTAAGAAT 58.087 29.630 0.00 0.00 0.00 2.40
3715 3956 0.543277 TGCCCTGTCATCATCACTCC 59.457 55.000 0.00 0.00 0.00 3.85
3716 3957 2.408271 TTGCCCTGTCATCATCACTC 57.592 50.000 0.00 0.00 0.00 3.51
3717 3958 2.224843 TGTTTGCCCTGTCATCATCACT 60.225 45.455 0.00 0.00 0.00 3.41
3718 3959 2.161855 TGTTTGCCCTGTCATCATCAC 58.838 47.619 0.00 0.00 0.00 3.06
3719 3960 2.224843 ACTGTTTGCCCTGTCATCATCA 60.225 45.455 0.00 0.00 0.00 3.07
3720 3961 2.440409 ACTGTTTGCCCTGTCATCATC 58.560 47.619 0.00 0.00 0.00 2.92
3721 3962 2.559668 CAACTGTTTGCCCTGTCATCAT 59.440 45.455 0.00 0.00 0.00 2.45
3722 3963 1.955778 CAACTGTTTGCCCTGTCATCA 59.044 47.619 0.00 0.00 0.00 3.07
3723 3964 2.712057 CAACTGTTTGCCCTGTCATC 57.288 50.000 0.00 0.00 0.00 2.92
3733 3974 1.610038 TCTGGCTGATGCAACTGTTTG 59.390 47.619 0.00 0.00 41.91 2.93
3734 3975 1.884579 CTCTGGCTGATGCAACTGTTT 59.115 47.619 0.00 0.00 41.91 2.83
3735 3976 1.531423 CTCTGGCTGATGCAACTGTT 58.469 50.000 0.00 0.00 41.91 3.16
3736 3977 0.322277 CCTCTGGCTGATGCAACTGT 60.322 55.000 0.00 0.00 41.91 3.55
3737 3978 0.035725 TCCTCTGGCTGATGCAACTG 60.036 55.000 0.00 0.00 41.91 3.16
3738 3979 0.252479 CTCCTCTGGCTGATGCAACT 59.748 55.000 0.00 0.00 41.91 3.16
3739 3980 0.035630 ACTCCTCTGGCTGATGCAAC 60.036 55.000 0.00 0.00 41.91 4.17
3740 3981 0.035725 CACTCCTCTGGCTGATGCAA 60.036 55.000 0.00 0.00 41.91 4.08
3741 3982 0.906282 TCACTCCTCTGGCTGATGCA 60.906 55.000 0.00 0.00 41.91 3.96
3742 3983 0.469070 ATCACTCCTCTGGCTGATGC 59.531 55.000 0.00 0.00 38.76 3.91
3743 3984 1.761198 TCATCACTCCTCTGGCTGATG 59.239 52.381 13.41 13.41 38.16 3.07
3744 3985 2.171568 TCATCACTCCTCTGGCTGAT 57.828 50.000 0.00 0.00 0.00 2.90
3745 3986 1.761198 CATCATCACTCCTCTGGCTGA 59.239 52.381 0.00 0.00 0.00 4.26
3746 3987 1.761198 TCATCATCACTCCTCTGGCTG 59.239 52.381 0.00 0.00 0.00 4.85
3818 4059 2.540973 GCGTCCAGTTTCACCTTCAAAC 60.541 50.000 0.00 0.00 34.47 2.93
3877 4118 0.471211 AGGTTCTGTTCGGTCCTGGA 60.471 55.000 0.00 0.00 0.00 3.86
3921 4162 3.097614 GCTACTCCTACAAGGACCTTGA 58.902 50.000 35.69 19.98 43.42 3.02
3922 4163 3.100671 AGCTACTCCTACAAGGACCTTG 58.899 50.000 29.13 29.13 40.06 3.61
3923 4164 3.100671 CAGCTACTCCTACAAGGACCTT 58.899 50.000 0.00 0.00 40.06 3.50
3924 4165 2.043252 ACAGCTACTCCTACAAGGACCT 59.957 50.000 0.00 0.00 40.06 3.85
3925 4166 2.458620 ACAGCTACTCCTACAAGGACC 58.541 52.381 0.00 0.00 40.06 4.46
3926 4167 4.021368 TGAAACAGCTACTCCTACAAGGAC 60.021 45.833 0.00 0.00 40.06 3.85
3928 4169 4.537135 TGAAACAGCTACTCCTACAAGG 57.463 45.455 0.00 0.00 36.46 3.61
3973 4231 4.400567 GGTCCCGTAGTACTACTCAACAAT 59.599 45.833 26.36 0.00 34.04 2.71
4051 4311 3.623060 GTCCATGTACCACTTGCAGTATG 59.377 47.826 0.00 0.00 40.87 2.39
4052 4312 3.263170 TGTCCATGTACCACTTGCAGTAT 59.737 43.478 0.00 0.00 0.00 2.12
4132 4392 1.465387 TGGTGCTTGGTTAATTACGCG 59.535 47.619 3.53 3.53 0.00 6.01
4159 4423 6.150140 GCTGATTCCCTCATGGTATATTTGTC 59.850 42.308 0.00 0.00 32.10 3.18
4245 4607 7.116075 TGGTTGTTTGTCATATATGGCTACTT 58.884 34.615 17.81 0.00 32.56 2.24
4384 4746 4.692228 TCTGATGCGCTCATTTACATGTA 58.308 39.130 9.73 0.08 32.10 2.29
4461 4823 0.846693 ATCCCTGTGTAATCCTGCCC 59.153 55.000 0.00 0.00 0.00 5.36
4605 5025 8.025243 TGTAACTAAACATCTTCCGTTGAATC 57.975 34.615 0.00 0.00 0.00 2.52
4661 5081 9.923143 GTTTACTATGGGAAAAGCTGTTAAATT 57.077 29.630 0.00 0.00 0.00 1.82
4662 5082 9.309224 AGTTTACTATGGGAAAAGCTGTTAAAT 57.691 29.630 0.00 0.00 0.00 1.40
4663 5083 8.700439 AGTTTACTATGGGAAAAGCTGTTAAA 57.300 30.769 0.00 0.00 0.00 1.52
4664 5084 9.444600 CTAGTTTACTATGGGAAAAGCTGTTAA 57.555 33.333 0.00 0.00 0.00 2.01
4665 5085 8.599792 ACTAGTTTACTATGGGAAAAGCTGTTA 58.400 33.333 0.00 0.00 0.00 2.41
4666 5086 7.459234 ACTAGTTTACTATGGGAAAAGCTGTT 58.541 34.615 0.00 0.00 0.00 3.16
4667 5087 7.017319 ACTAGTTTACTATGGGAAAAGCTGT 57.983 36.000 0.00 0.00 0.00 4.40
4668 5088 7.494952 GGTACTAGTTTACTATGGGAAAAGCTG 59.505 40.741 0.00 0.00 0.00 4.24
4669 5089 7.181485 TGGTACTAGTTTACTATGGGAAAAGCT 59.819 37.037 0.00 0.00 0.00 3.74
4670 5090 7.333323 TGGTACTAGTTTACTATGGGAAAAGC 58.667 38.462 0.00 0.00 0.00 3.51
4671 5091 9.901172 ATTGGTACTAGTTTACTATGGGAAAAG 57.099 33.333 0.00 0.00 0.00 2.27
4676 5096 9.939802 GGAATATTGGTACTAGTTTACTATGGG 57.060 37.037 0.00 0.00 0.00 4.00
4697 5117 5.708544 AGATTGCCCTTCATGATTGGAATA 58.291 37.500 13.71 1.97 0.00 1.75


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

AutoCloner maintained by Alex Coulton.