Multiple sequence alignment - TraesCS2B01G470400

Loading Multiple Alignment...

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 TraesCS2B01G470400 chr2B 100.000 4850 0 0 1 4850 666649066 666653915 0.000000e+00 8957
1 TraesCS2B01G470400 chr2B 79.650 742 119 19 17 732 58546932 58547667 5.600000e-139 505
2 TraesCS2B01G470400 chr2B 77.732 732 115 21 17 732 58352888 58353587 5.850000e-109 405
3 TraesCS2B01G470400 chr2B 92.593 162 9 2 2402 2560 585712655 585712494 3.780000e-56 230
4 TraesCS2B01G470400 chr2A 92.088 1959 110 21 2903 4841 698825711 698827644 0.000000e+00 2717
5 TraesCS2B01G470400 chr2A 89.532 1882 143 25 17 1876 698822773 698824622 0.000000e+00 2335
6 TraesCS2B01G470400 chr2A 95.283 530 22 2 1871 2398 698824763 698825291 0.000000e+00 837
7 TraesCS2B01G470400 chr2A 90.358 363 32 2 2559 2920 698825337 698825697 1.580000e-129 473
8 TraesCS2B01G470400 chr2A 73.588 655 148 19 10 648 488932129 488932774 1.360000e-55 228
9 TraesCS2B01G470400 chr2D 91.335 1985 110 24 2903 4850 558238882 558240841 0.000000e+00 2656
10 TraesCS2B01G470400 chr2D 89.393 1103 74 16 795 1876 558236691 558237771 0.000000e+00 1349
11 TraesCS2B01G470400 chr2D 95.490 510 20 2 1891 2398 558237956 558238464 0.000000e+00 811
12 TraesCS2B01G470400 chr2D 91.160 362 28 3 2559 2919 558238510 558238868 5.640000e-134 488
13 TraesCS2B01G470400 chr2D 81.818 528 69 16 276 793 558236098 558236608 7.510000e-113 418
14 TraesCS2B01G470400 chr2D 92.405 158 10 1 2402 2557 318563734 318563891 1.760000e-54 224
15 TraesCS2B01G470400 chr2D 91.975 162 10 2 2402 2560 498473158 498472997 1.760000e-54 224
16 TraesCS2B01G470400 chr4D 80.144 695 98 24 36 705 51298409 51297730 2.620000e-132 483
17 TraesCS2B01G470400 chr4D 90.741 162 12 2 2402 2560 75266909 75266748 3.800000e-51 213
18 TraesCS2B01G470400 chr4D 76.943 386 70 12 288 658 9448804 9448423 8.230000e-48 202
19 TraesCS2B01G470400 chr7A 76.271 708 138 25 14 704 692216147 692216841 2.780000e-92 350
20 TraesCS2B01G470400 chr4B 76.872 601 97 24 171 734 660716726 660716131 7.890000e-78 302
21 TraesCS2B01G470400 chr4B 79.191 173 27 4 169 332 18098064 18097892 1.430000e-20 111
22 TraesCS2B01G470400 chr7D 93.210 162 8 2 2402 2560 566026736 566026575 8.120000e-58 235
23 TraesCS2B01G470400 chr7B 91.195 159 11 2 2402 2557 730165978 730166136 3.800000e-51 213
24 TraesCS2B01G470400 chr7B 89.017 173 16 3 2402 2572 428829535 428829364 1.370000e-50 211
25 TraesCS2B01G470400 chr3B 89.759 166 14 2 2398 2560 251650681 251650516 4.920000e-50 209
26 TraesCS2B01G470400 chr6A 86.559 186 19 5 2378 2557 108947676 108947861 2.960000e-47 200
27 TraesCS2B01G470400 chr6A 73.716 331 73 10 258 579 143975805 143976130 3.070000e-22 117


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 TraesCS2B01G470400 chr2B 666649066 666653915 4849 False 8957.0 8957 100.00000 1 4850 1 chr2B.!!$F3 4849
1 TraesCS2B01G470400 chr2B 58546932 58547667 735 False 505.0 505 79.65000 17 732 1 chr2B.!!$F2 715
2 TraesCS2B01G470400 chr2B 58352888 58353587 699 False 405.0 405 77.73200 17 732 1 chr2B.!!$F1 715
3 TraesCS2B01G470400 chr2A 698822773 698827644 4871 False 1590.5 2717 91.81525 17 4841 4 chr2A.!!$F2 4824
4 TraesCS2B01G470400 chr2A 488932129 488932774 645 False 228.0 228 73.58800 10 648 1 chr2A.!!$F1 638
5 TraesCS2B01G470400 chr2D 558236098 558240841 4743 False 1144.4 2656 89.83920 276 4850 5 chr2D.!!$F2 4574
6 TraesCS2B01G470400 chr4D 51297730 51298409 679 True 483.0 483 80.14400 36 705 1 chr4D.!!$R2 669
7 TraesCS2B01G470400 chr7A 692216147 692216841 694 False 350.0 350 76.27100 14 704 1 chr7A.!!$F1 690
8 TraesCS2B01G470400 chr4B 660716131 660716726 595 True 302.0 302 76.87200 171 734 1 chr4B.!!$R2 563

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
134 138 0.541863 GCAAATCCCCTCTCCTTCGA 59.458 55.0 0.00 0.00 0.00 3.71 F
878 1026 1.059913 GTGATAGATCCCCCACCCTG 58.940 60.0 0.00 0.00 0.00 4.45 F
1511 1680 0.595095 GCCACTCAGCTGTTTTCTGG 59.405 55.0 14.67 12.49 32.63 3.86 F
1671 1840 0.969894 AGTTAACCGTCTGCAGAGCT 59.030 50.0 18.89 4.32 0.00 4.09 F
3022 3403 0.107508 CAGGTGTATGACTGGCCCAG 60.108 60.0 9.83 9.83 37.52 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1191 1352 1.807142 GGTCCTTAGCACAGAACAAGC 59.193 52.381 0.00 0.0 0.0 4.01 R
2754 3098 0.034089 CACCCATGTTCCTTCCCTCC 60.034 60.000 0.00 0.0 0.0 4.30 R
2988 3369 0.107831 ACCTGTCTGCCAAGCGTTAA 59.892 50.000 0.00 0.0 0.0 2.01 R
3200 3587 0.960364 AGCATTACGTGGCCTTGGTG 60.960 55.000 3.32 0.0 0.0 4.17 R
3979 4374 2.676471 ACCCATCAGTTTGCCCGC 60.676 61.111 0.00 0.0 0.0 6.13 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
24 25 4.700332 CACCGCTCGTTAAATTTTTACGA 58.300 39.130 18.75 18.75 0.00 3.43
32 33 4.154556 CGTTAAATTTTTACGAGAGGCCCA 59.845 41.667 13.73 0.00 0.00 5.36
34 35 4.718940 AAATTTTTACGAGAGGCCCATG 57.281 40.909 0.00 0.00 0.00 3.66
62 63 4.119862 CCCCTGAATCCGCAATATATACG 58.880 47.826 1.97 1.97 0.00 3.06
66 67 6.461648 CCCTGAATCCGCAATATATACGAGAT 60.462 42.308 9.09 7.52 0.00 2.75
85 86 5.452077 CGAGATCGAGGAGATTTTAGGGTTT 60.452 44.000 0.00 0.00 40.26 3.27
103 104 3.442273 GGTTTGCATCGTTCATTTCCCTA 59.558 43.478 0.00 0.00 0.00 3.53
112 116 3.388024 CGTTCATTTCCCTATCTCCTCCA 59.612 47.826 0.00 0.00 0.00 3.86
134 138 0.541863 GCAAATCCCCTCTCCTTCGA 59.458 55.000 0.00 0.00 0.00 3.71
167 173 2.563798 CCTTCGGCAGCCTTTTGCA 61.564 57.895 10.54 0.00 45.86 4.08
209 215 1.888436 ATCCCTGATGTCGTGCACGT 61.888 55.000 35.74 19.73 40.80 4.49
414 435 2.279517 CCGAATCTTCTCGCCCGG 60.280 66.667 0.00 0.00 37.51 5.73
615 659 9.391006 TGATGCGTAGATCTAGGTTTAATTTTT 57.609 29.630 20.49 0.23 0.00 1.94
662 722 5.628193 CGTATGAACTCCGGTGATGTAATAC 59.372 44.000 11.17 9.24 0.00 1.89
663 723 5.607939 ATGAACTCCGGTGATGTAATACA 57.392 39.130 11.17 0.00 0.00 2.29
665 725 5.356426 TGAACTCCGGTGATGTAATACATG 58.644 41.667 11.03 0.00 39.27 3.21
666 726 4.336889 ACTCCGGTGATGTAATACATGG 57.663 45.455 11.03 5.94 39.27 3.66
667 727 3.067106 CTCCGGTGATGTAATACATGGC 58.933 50.000 11.03 3.25 39.27 4.40
749 810 3.687102 CTGCCCGTCGGTGGTACA 61.687 66.667 11.06 0.00 0.00 2.90
767 828 8.118607 GGTGGTACAGTAAATTTAGTTTATCGC 58.881 37.037 11.93 11.93 41.80 4.58
768 829 7.842721 GTGGTACAGTAAATTTAGTTTATCGCG 59.157 37.037 0.00 0.00 41.80 5.87
836 978 2.099098 CCAACTGCTCGTGGAAAAACTT 59.901 45.455 0.00 0.00 0.00 2.66
873 1015 1.140312 GCCAAGTGATAGATCCCCCA 58.860 55.000 0.00 0.00 0.00 4.96
878 1026 1.059913 GTGATAGATCCCCCACCCTG 58.940 60.000 0.00 0.00 0.00 4.45
1114 1275 3.013921 TCATGGGAACGTATTGGCTTTC 58.986 45.455 0.00 0.00 0.00 2.62
1144 1305 5.415701 AGAATCAGATGCGTGTTAATTTGGT 59.584 36.000 0.00 0.00 0.00 3.67
1158 1319 4.360951 AATTTGGTCACCGGAACTTCTA 57.639 40.909 9.46 0.00 0.00 2.10
1191 1352 3.571401 AGACCAAAGAGATTTGCACCTTG 59.429 43.478 0.00 0.00 0.00 3.61
1396 1563 7.581213 TGGATATCCAATTGCTCGTATTTTT 57.419 32.000 22.52 0.00 44.35 1.94
1501 1670 0.955919 GTACCCAGTTGCCACTCAGC 60.956 60.000 0.00 0.00 0.00 4.26
1507 1676 1.406539 CAGTTGCCACTCAGCTGTTTT 59.593 47.619 14.67 0.00 45.45 2.43
1511 1680 0.595095 GCCACTCAGCTGTTTTCTGG 59.405 55.000 14.67 12.49 32.63 3.86
1520 1689 4.578928 TCAGCTGTTTTCTGGGAGTTTTAC 59.421 41.667 14.67 0.00 32.63 2.01
1523 1692 5.067805 AGCTGTTTTCTGGGAGTTTTACTTG 59.932 40.000 0.00 0.00 0.00 3.16
1544 1713 1.869767 CTTCTGTTCTGTCACAGGTGC 59.130 52.381 4.57 0.00 43.92 5.01
1671 1840 0.969894 AGTTAACCGTCTGCAGAGCT 59.030 50.000 18.89 4.32 0.00 4.09
1751 1920 2.885135 TCACATCTGGAGCACCAAAT 57.115 45.000 3.90 0.00 46.32 2.32
1762 1932 5.841810 TGGAGCACCAAATTTTTGAAGTAG 58.158 37.500 0.00 0.00 43.91 2.57
1764 1934 6.127196 TGGAGCACCAAATTTTTGAAGTAGTT 60.127 34.615 0.00 0.00 43.91 2.24
1774 1944 8.409358 AATTTTTGAAGTAGTTGAGCATAGGT 57.591 30.769 0.00 0.00 0.00 3.08
1832 2002 3.539604 GTGGTAGAGAACGAGTAGCCTA 58.460 50.000 0.00 0.00 0.00 3.93
1833 2003 3.312146 GTGGTAGAGAACGAGTAGCCTAC 59.688 52.174 0.00 0.00 0.00 3.18
1841 2011 5.411781 AGAACGAGTAGCCTACTTCATTTG 58.588 41.667 5.74 0.00 39.59 2.32
1842 2012 4.803098 ACGAGTAGCCTACTTCATTTGT 57.197 40.909 5.74 0.00 39.59 2.83
1848 2018 6.534634 AGTAGCCTACTTCATTTGTTGTTCT 58.465 36.000 0.00 0.00 34.86 3.01
2189 2530 8.049117 TGATTATGCAGTGAAGATTCTAAAGGT 58.951 33.333 0.00 0.00 0.00 3.50
2301 2642 3.270027 TGGAGTATTCTTCATTGCCACG 58.730 45.455 0.00 0.00 0.00 4.94
2337 2678 9.354673 TCAGAAAGGGAATATAAAACCATCATC 57.645 33.333 0.00 0.00 0.00 2.92
2374 2717 4.195416 GCTCTGCCTAGCAAATAGAAGTT 58.805 43.478 2.69 0.00 42.30 2.66
2378 2721 6.707290 TCTGCCTAGCAAATAGAAGTTACAA 58.293 36.000 0.00 0.00 38.41 2.41
2382 2725 7.148255 TGCCTAGCAAATAGAAGTTACAACATG 60.148 37.037 0.00 0.00 34.76 3.21
2392 2735 6.223852 AGAAGTTACAACATGTAGTGTCCTG 58.776 40.000 6.45 0.00 41.14 3.86
2398 2741 1.346395 ACATGTAGTGTCCTGCCGAAA 59.654 47.619 0.00 0.00 35.77 3.46
2399 2742 2.027192 ACATGTAGTGTCCTGCCGAAAT 60.027 45.455 0.00 0.00 35.77 2.17
2400 2743 2.093306 TGTAGTGTCCTGCCGAAATG 57.907 50.000 0.00 0.00 0.00 2.32
2401 2744 1.346395 TGTAGTGTCCTGCCGAAATGT 59.654 47.619 0.00 0.00 0.00 2.71
2403 2746 2.094762 AGTGTCCTGCCGAAATGTAC 57.905 50.000 0.00 0.00 0.00 2.90
2404 2747 1.623811 AGTGTCCTGCCGAAATGTACT 59.376 47.619 0.00 0.00 0.00 2.73
2406 2749 1.066430 TGTCCTGCCGAAATGTACTCC 60.066 52.381 0.00 0.00 0.00 3.85
2407 2750 1.207329 GTCCTGCCGAAATGTACTCCT 59.793 52.381 0.00 0.00 0.00 3.69
2408 2751 1.480954 TCCTGCCGAAATGTACTCCTC 59.519 52.381 0.00 0.00 0.00 3.71
2409 2752 1.482593 CCTGCCGAAATGTACTCCTCT 59.517 52.381 0.00 0.00 0.00 3.69
2410 2753 2.544685 CTGCCGAAATGTACTCCTCTG 58.455 52.381 0.00 0.00 0.00 3.35
2411 2754 1.899814 TGCCGAAATGTACTCCTCTGT 59.100 47.619 0.00 0.00 0.00 3.41
2413 2756 2.930682 GCCGAAATGTACTCCTCTGTTC 59.069 50.000 0.00 0.00 0.00 3.18
2414 2757 3.522553 CCGAAATGTACTCCTCTGTTCC 58.477 50.000 0.00 0.00 0.00 3.62
2415 2758 3.195825 CCGAAATGTACTCCTCTGTTCCT 59.804 47.826 0.00 0.00 0.00 3.36
2416 2759 4.401519 CCGAAATGTACTCCTCTGTTCCTA 59.598 45.833 0.00 0.00 0.00 2.94
2418 2761 6.395629 CGAAATGTACTCCTCTGTTCCTAAA 58.604 40.000 0.00 0.00 0.00 1.85
2419 2762 7.042335 CGAAATGTACTCCTCTGTTCCTAAAT 58.958 38.462 0.00 0.00 0.00 1.40
2420 2763 7.010552 CGAAATGTACTCCTCTGTTCCTAAATG 59.989 40.741 0.00 0.00 0.00 2.32
2421 2764 6.875972 ATGTACTCCTCTGTTCCTAAATGT 57.124 37.500 0.00 0.00 0.00 2.71
2424 2767 7.837863 TGTACTCCTCTGTTCCTAAATGTAAG 58.162 38.462 0.00 0.00 0.00 2.34
2425 2768 5.735766 ACTCCTCTGTTCCTAAATGTAAGC 58.264 41.667 0.00 0.00 0.00 3.09
2426 2769 5.099042 TCCTCTGTTCCTAAATGTAAGCC 57.901 43.478 0.00 0.00 0.00 4.35
2427 2770 4.783227 TCCTCTGTTCCTAAATGTAAGCCT 59.217 41.667 0.00 0.00 0.00 4.58
2428 2771 5.250774 TCCTCTGTTCCTAAATGTAAGCCTT 59.749 40.000 0.00 0.00 0.00 4.35
2430 2773 6.434340 CCTCTGTTCCTAAATGTAAGCCTTTT 59.566 38.462 0.00 0.00 0.00 2.27
2431 2774 7.039714 CCTCTGTTCCTAAATGTAAGCCTTTTT 60.040 37.037 0.00 0.00 0.00 1.94
2433 2776 9.010029 TCTGTTCCTAAATGTAAGCCTTTTTAG 57.990 33.333 1.71 1.71 33.47 1.85
2434 2777 8.927675 TGTTCCTAAATGTAAGCCTTTTTAGA 57.072 30.769 8.15 0.00 34.90 2.10
2435 2778 9.010029 TGTTCCTAAATGTAAGCCTTTTTAGAG 57.990 33.333 8.15 1.42 34.90 2.43
2436 2779 9.227777 GTTCCTAAATGTAAGCCTTTTTAGAGA 57.772 33.333 8.15 3.15 34.90 3.10
2437 2780 9.975218 TTCCTAAATGTAAGCCTTTTTAGAGAT 57.025 29.630 8.15 0.00 34.90 2.75
2438 2781 9.975218 TCCTAAATGTAAGCCTTTTTAGAGATT 57.025 29.630 8.15 0.00 34.90 2.40
2441 2784 8.650143 AAATGTAAGCCTTTTTAGAGATTCCA 57.350 30.769 0.00 0.00 0.00 3.53
2442 2785 8.650143 AATGTAAGCCTTTTTAGAGATTCCAA 57.350 30.769 0.00 0.00 0.00 3.53
2445 2788 9.174166 TGTAAGCCTTTTTAGAGATTCCAATAC 57.826 33.333 0.00 0.00 0.00 1.89
2446 2789 9.174166 GTAAGCCTTTTTAGAGATTCCAATACA 57.826 33.333 0.00 0.00 0.00 2.29
2447 2790 7.872113 AGCCTTTTTAGAGATTCCAATACAG 57.128 36.000 0.00 0.00 0.00 2.74
2448 2791 7.633789 AGCCTTTTTAGAGATTCCAATACAGA 58.366 34.615 0.00 0.00 0.00 3.41
2449 2792 7.554476 AGCCTTTTTAGAGATTCCAATACAGAC 59.446 37.037 0.00 0.00 0.00 3.51
2450 2793 7.554476 GCCTTTTTAGAGATTCCAATACAGACT 59.446 37.037 0.00 0.00 0.00 3.24
2457 2800 7.877003 AGAGATTCCAATACAGACTACATACG 58.123 38.462 0.00 0.00 0.00 3.06
2458 2801 6.982852 AGATTCCAATACAGACTACATACGG 58.017 40.000 0.00 0.00 0.00 4.02
2459 2802 6.776116 AGATTCCAATACAGACTACATACGGA 59.224 38.462 0.00 0.00 0.00 4.69
2460 2803 6.387041 TTCCAATACAGACTACATACGGAG 57.613 41.667 0.00 0.00 0.00 4.63
2461 2804 4.277672 TCCAATACAGACTACATACGGAGC 59.722 45.833 0.00 0.00 0.00 4.70
2462 2805 4.037565 CCAATACAGACTACATACGGAGCA 59.962 45.833 0.00 0.00 0.00 4.26
2463 2806 5.451381 CCAATACAGACTACATACGGAGCAA 60.451 44.000 0.00 0.00 0.00 3.91
2464 2807 5.847111 ATACAGACTACATACGGAGCAAA 57.153 39.130 0.00 0.00 0.00 3.68
2465 2808 4.530710 ACAGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2466 2809 5.086104 ACAGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2467 2810 4.870426 ACAGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2468 2811 5.109210 CAGACTACATACGGAGCAAAATGA 58.891 41.667 0.00 0.00 0.00 2.57
2469 2812 5.233050 CAGACTACATACGGAGCAAAATGAG 59.767 44.000 0.00 0.00 0.00 2.90
2470 2813 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2471 2814 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2472 2815 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2473 2816 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2474 2817 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2475 2818 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2476 2819 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2477 2820 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2478 2821 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2479 2822 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2480 2823 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2493 2836 8.485976 AGTGAATCTACACTCTAAAATGCTTC 57.514 34.615 0.00 0.00 46.36 3.86
2494 2837 8.317679 AGTGAATCTACACTCTAAAATGCTTCT 58.682 33.333 0.00 0.00 46.36 2.85
2495 2838 9.587772 GTGAATCTACACTCTAAAATGCTTCTA 57.412 33.333 0.00 0.00 37.73 2.10
2555 2898 8.959705 AAGGTCTTATATTTAGAAACGGAAGG 57.040 34.615 0.00 0.00 0.00 3.46
2556 2899 8.315220 AGGTCTTATATTTAGAAACGGAAGGA 57.685 34.615 0.00 0.00 0.00 3.36
2557 2900 8.202811 AGGTCTTATATTTAGAAACGGAAGGAC 58.797 37.037 0.00 0.00 0.00 3.85
2558 2901 8.202811 GGTCTTATATTTAGAAACGGAAGGACT 58.797 37.037 0.00 0.00 0.00 3.85
2566 2909 3.260884 AGAAACGGAAGGACTAATGCTGA 59.739 43.478 0.00 0.00 0.00 4.26
2577 2920 5.869888 AGGACTAATGCTGAAACTCTTAACG 59.130 40.000 0.00 0.00 0.00 3.18
2652 2996 3.500448 TGGTTGTTATGGTCTTGAGCA 57.500 42.857 4.96 4.96 0.00 4.26
2653 2997 3.826524 TGGTTGTTATGGTCTTGAGCAA 58.173 40.909 6.60 0.00 0.00 3.91
2663 3007 4.776349 TGGTCTTGAGCAAAAGTACAGAA 58.224 39.130 0.00 0.00 0.00 3.02
2682 3026 6.190587 ACAGAAAAATAGGAATGGGAAGGAG 58.809 40.000 0.00 0.00 0.00 3.69
2685 3029 3.872459 AATAGGAATGGGAAGGAGCAG 57.128 47.619 0.00 0.00 0.00 4.24
2687 3031 1.454663 GGAATGGGAAGGAGCAGGC 60.455 63.158 0.00 0.00 0.00 4.85
2690 3034 2.505364 AATGGGAAGGAGCAGGCCAC 62.505 60.000 5.01 0.00 0.00 5.01
2691 3035 3.650950 GGGAAGGAGCAGGCCACA 61.651 66.667 5.01 0.00 0.00 4.17
2714 3058 1.298339 GTGCACTGTTGTGGCGTTC 60.298 57.895 10.32 0.00 43.97 3.95
2810 3154 7.586349 TCTTGCTTCCCCTATTTGATTATTCT 58.414 34.615 0.00 0.00 0.00 2.40
2819 3163 8.200792 CCCCTATTTGATTATTCTATCTCCTCG 58.799 40.741 0.00 0.00 0.00 4.63
2821 3165 7.433719 CCTATTTGATTATTCTATCTCCTCGCG 59.566 40.741 0.00 0.00 0.00 5.87
2843 3187 2.230660 ACCAGGTTGCAAGTAAGAAGC 58.769 47.619 0.00 0.00 0.00 3.86
2845 3189 2.227388 CCAGGTTGCAAGTAAGAAGCAG 59.773 50.000 0.00 0.00 39.72 4.24
2864 3209 4.457257 AGCAGTGAACAAAAGCTAGAATCC 59.543 41.667 0.00 0.00 33.06 3.01
2922 3298 7.050377 TCTTTGACATCCAATTCCTAGCTTAG 58.950 38.462 0.00 0.00 34.23 2.18
2928 3304 2.173569 CCAATTCCTAGCTTAGTGGGCT 59.826 50.000 0.00 0.00 43.02 5.19
2930 3306 4.141482 CCAATTCCTAGCTTAGTGGGCTAA 60.141 45.833 0.00 0.00 41.02 3.09
2953 3334 6.443995 AGGAGTCCTAGTCCTCTAGTAATC 57.556 45.833 10.94 0.00 44.63 1.75
2977 3358 4.797693 CATCAGTTGCTGCTTCTATCTG 57.202 45.455 0.00 0.00 0.00 2.90
2987 3368 2.158856 TGCTTCTATCTGTGATGCCAGG 60.159 50.000 0.00 0.00 34.85 4.45
2988 3369 2.158842 GCTTCTATCTGTGATGCCAGGT 60.159 50.000 0.00 0.00 33.14 4.00
3018 3399 2.009042 GCAGACAGGTGTATGACTGGC 61.009 57.143 8.90 0.00 43.15 4.85
3019 3400 0.905357 AGACAGGTGTATGACTGGCC 59.095 55.000 0.00 0.00 43.88 5.36
3020 3401 0.107654 GACAGGTGTATGACTGGCCC 60.108 60.000 0.00 0.00 36.74 5.80
3021 3402 0.840288 ACAGGTGTATGACTGGCCCA 60.840 55.000 0.00 0.00 39.00 5.36
3022 3403 0.107508 CAGGTGTATGACTGGCCCAG 60.108 60.000 9.83 9.83 37.52 4.45
3024 3405 0.392998 GGTGTATGACTGGCCCAGTG 60.393 60.000 23.85 0.00 45.44 3.66
3025 3406 0.392998 GTGTATGACTGGCCCAGTGG 60.393 60.000 23.85 0.63 45.44 4.00
3044 3425 1.842007 CCCTGGCTCCATGCTACAT 59.158 57.895 0.00 0.00 42.39 2.29
3060 3441 7.172190 CCATGCTACATTCTGTTATCTACTTGG 59.828 40.741 0.00 0.00 0.00 3.61
3072 3459 9.817809 CTGTTATCTACTTGGCTTGTTCTATTA 57.182 33.333 0.00 0.00 0.00 0.98
3088 3475 6.826231 TGTTCTATTAGCAATTTTCCATCGGA 59.174 34.615 0.00 0.00 0.00 4.55
3094 3481 2.098117 GCAATTTTCCATCGGAGGACTG 59.902 50.000 0.00 0.00 37.42 3.51
3103 3490 5.667466 TCCATCGGAGGACTGTTTATTAAC 58.333 41.667 0.00 0.00 31.23 2.01
3109 3496 7.669427 TCGGAGGACTGTTTATTAACAACTTA 58.331 34.615 0.00 0.00 43.33 2.24
3121 3508 9.856162 TTTATTAACAACTTAACCTCCTTGAGT 57.144 29.630 0.00 0.00 29.97 3.41
3182 3569 1.009829 CAAGATGGTAAGCCTGACGC 58.990 55.000 0.00 0.00 35.27 5.19
3200 3587 1.444895 CGCAAGGCATCCAAAGTGC 60.445 57.895 0.00 0.00 41.78 4.40
3249 3636 8.840200 ACTATGATGAAGGTTTAGAGGTAAGA 57.160 34.615 0.00 0.00 0.00 2.10
3263 3650 4.019321 AGAGGTAAGAAGCCAAATGCAGTA 60.019 41.667 0.00 0.00 44.83 2.74
3265 3652 4.010349 GGTAAGAAGCCAAATGCAGTAGT 58.990 43.478 0.00 0.00 44.83 2.73
3266 3653 4.459337 GGTAAGAAGCCAAATGCAGTAGTT 59.541 41.667 0.00 0.00 44.83 2.24
3267 3654 4.773323 AAGAAGCCAAATGCAGTAGTTC 57.227 40.909 0.00 0.00 44.83 3.01
3268 3655 3.754965 AGAAGCCAAATGCAGTAGTTCA 58.245 40.909 0.00 0.00 44.83 3.18
3269 3656 4.338879 AGAAGCCAAATGCAGTAGTTCAT 58.661 39.130 0.00 0.00 44.83 2.57
3270 3657 4.397417 AGAAGCCAAATGCAGTAGTTCATC 59.603 41.667 0.00 0.00 44.83 2.92
3274 3669 4.521146 CCAAATGCAGTAGTTCATCTCCT 58.479 43.478 0.00 0.00 0.00 3.69
3332 3727 8.600449 TTTTGACAACCAAATATTTGTGGATC 57.400 30.769 23.24 16.15 43.59 3.36
3492 3887 7.553044 AGAACCATTATAGAACCTTTACAGTGC 59.447 37.037 0.00 0.00 0.00 4.40
3557 3952 7.680442 AACAAAGTATTTTGGTTTGCACTTT 57.320 28.000 14.38 0.00 41.35 2.66
3606 4001 8.934023 TGTAAAGGTTCTTCAAATGAATACCT 57.066 30.769 17.61 17.61 44.16 3.08
3610 4005 9.588096 AAAGGTTCTTCAAATGAATACCTTAGT 57.412 29.630 26.39 17.31 46.57 2.24
3611 4006 9.588096 AAGGTTCTTCAAATGAATACCTTAGTT 57.412 29.630 25.68 12.96 46.07 2.24
3612 4007 9.014297 AGGTTCTTCAAATGAATACCTTAGTTG 57.986 33.333 17.61 0.00 41.86 3.16
3659 4054 5.163269 TGCTAGTGCTGGAAGTATGAATCAT 60.163 40.000 0.00 0.00 40.48 2.45
3844 4239 2.098614 TGCAAGGAGAAAGTGCAACAA 58.901 42.857 0.00 0.00 44.88 2.83
3923 4318 9.570468 AATTCATATAGTGCAGACATCTGAATT 57.430 29.630 13.15 15.50 46.59 2.17
3925 4320 7.729116 TCATATAGTGCAGACATCTGAATTGA 58.271 34.615 13.15 2.92 46.59 2.57
3979 4374 5.080969 TGAAACTACAGGGAGTATTTCGG 57.919 43.478 0.00 0.00 35.41 4.30
4017 4412 2.235155 TGCTCTATTCAACTAACCGGCA 59.765 45.455 0.00 0.00 0.00 5.69
4018 4413 2.866762 GCTCTATTCAACTAACCGGCAG 59.133 50.000 0.00 0.62 0.00 4.85
4021 4416 1.904287 ATTCAACTAACCGGCAGCAA 58.096 45.000 0.00 0.00 0.00 3.91
4124 4524 4.740334 GCCATCAGCTCCAAAAACTTTCAA 60.740 41.667 0.00 0.00 38.99 2.69
4181 4581 1.863454 GCTGAGTGGCATACGATTCTG 59.137 52.381 0.00 0.00 0.00 3.02
4182 4582 1.863454 CTGAGTGGCATACGATTCTGC 59.137 52.381 0.00 0.00 37.66 4.26
4262 4672 6.320672 CCTAGAAGAAATCAACTGATGGCATT 59.679 38.462 0.00 0.00 34.49 3.56
4265 4675 3.449737 AGAAATCAACTGATGGCATTGGG 59.550 43.478 0.00 0.00 34.49 4.12
4274 4684 2.446285 TGATGGCATTGGGATGGTATCA 59.554 45.455 0.00 0.00 33.72 2.15
4284 4694 7.014615 GCATTGGGATGGTATCAACTAGAAATT 59.985 37.037 0.00 0.00 33.72 1.82
4307 4717 6.139679 TCCATTACCTTGGACATCTTTCTT 57.860 37.500 0.00 0.00 40.90 2.52
4334 4744 3.697542 TCAAGATGTATTGCTGCAATGCT 59.302 39.130 32.82 22.60 37.36 3.79
4402 4812 6.645306 TCAACATATTAGAATTGGTGACCGA 58.355 36.000 0.00 0.00 32.38 4.69
4465 4875 4.091453 CAGTAACCTGGGTAAAATTGCG 57.909 45.455 0.00 0.00 34.90 4.85
4494 4904 5.580691 ACGAATGAGAACGATGCTGAAAATA 59.419 36.000 0.00 0.00 0.00 1.40
4553 4963 2.687935 CGGCATGCATTAGGTAGGTTTT 59.312 45.455 21.36 0.00 0.00 2.43
4583 4993 2.747446 CCGGTGAAATGGACCTAACTTG 59.253 50.000 0.00 0.00 0.00 3.16
4590 5000 3.567478 ATGGACCTAACTTGGATGAGC 57.433 47.619 0.00 0.00 0.00 4.26
4630 5040 5.741388 ATGATTTGCAATCCTTCGTAGTC 57.259 39.130 0.00 0.00 0.00 2.59
4654 5064 5.520288 CGTAGCTAGTGTTGCTTCATACATT 59.480 40.000 0.00 0.00 41.46 2.71
4680 5090 1.140852 TCTGAAATGCGGTATCCCCTG 59.859 52.381 0.00 0.00 0.00 4.45
4713 5124 6.728200 TGAAGTAAATCTCTGCAAGTTTGTG 58.272 36.000 0.00 0.00 33.76 3.33
4716 5127 4.574599 AAATCTCTGCAAGTTTGTGGTC 57.425 40.909 0.00 0.00 33.76 4.02
4773 5184 8.839947 GGAACCAAAACAAATTGAAAAATCTG 57.160 30.769 0.00 0.00 31.84 2.90
4778 5189 9.493206 CCAAAACAAATTGAAAAATCTGTTGAG 57.507 29.630 0.00 0.00 29.89 3.02
4832 5243 0.603569 ACTCCTCGGTGTCACATCAC 59.396 55.000 5.12 0.00 37.57 3.06
4842 5253 1.148310 GTCACATCACAACTGTCGGG 58.852 55.000 0.00 0.00 0.00 5.14
4843 5254 1.044611 TCACATCACAACTGTCGGGA 58.955 50.000 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.341318 AAAATTTAACGAGCGGTGCC 57.659 45.000 0.00 0.00 0.00 5.01
4 5 5.194199 TCTCGTAAAAATTTAACGAGCGG 57.806 39.130 31.55 19.95 40.22 5.52
5 6 5.245850 CCTCTCGTAAAAATTTAACGAGCG 58.754 41.667 31.55 28.13 40.22 5.03
6 7 5.020128 GCCTCTCGTAAAAATTTAACGAGC 58.980 41.667 31.55 23.92 40.22 5.03
7 8 5.446875 GGGCCTCTCGTAAAAATTTAACGAG 60.447 44.000 31.03 31.03 40.88 4.18
8 9 4.392754 GGGCCTCTCGTAAAAATTTAACGA 59.607 41.667 20.85 20.85 0.00 3.85
9 10 4.154556 TGGGCCTCTCGTAAAAATTTAACG 59.845 41.667 16.02 16.02 0.00 3.18
10 11 5.632244 TGGGCCTCTCGTAAAAATTTAAC 57.368 39.130 4.53 0.00 0.00 2.01
11 12 5.946972 TCATGGGCCTCTCGTAAAAATTTAA 59.053 36.000 4.53 0.00 0.00 1.52
12 13 5.502079 TCATGGGCCTCTCGTAAAAATTTA 58.498 37.500 4.53 0.00 0.00 1.40
24 25 4.115199 GGCGGTTCATGGGCCTCT 62.115 66.667 4.53 0.00 43.52 3.69
32 33 1.227383 GGATTCAGGGGCGGTTCAT 59.773 57.895 0.00 0.00 0.00 2.57
34 35 2.513897 CGGATTCAGGGGCGGTTC 60.514 66.667 0.00 0.00 0.00 3.62
62 63 5.538849 AACCCTAAAATCTCCTCGATCTC 57.461 43.478 0.00 0.00 0.00 2.75
66 67 3.008594 TGCAAACCCTAAAATCTCCTCGA 59.991 43.478 0.00 0.00 0.00 4.04
85 86 4.380531 GAGATAGGGAAATGAACGATGCA 58.619 43.478 0.00 0.00 0.00 3.96
103 104 0.181350 GGATTTGCGGTGGAGGAGAT 59.819 55.000 0.00 0.00 0.00 2.75
112 116 1.208165 AAGGAGAGGGGATTTGCGGT 61.208 55.000 0.00 0.00 0.00 5.68
134 138 1.204941 CGAAGGAGAGGGATTTGTCGT 59.795 52.381 0.00 0.00 0.00 4.34
209 215 4.284550 GCCACCCCTTCCAGCACA 62.285 66.667 0.00 0.00 0.00 4.57
213 219 4.101448 CTCGGCCACCCCTTCCAG 62.101 72.222 2.24 0.00 0.00 3.86
334 355 1.227853 GAAGAGGGTGGCGTGTGTT 60.228 57.895 0.00 0.00 0.00 3.32
342 363 4.020617 TGCTGCGGAAGAGGGTGG 62.021 66.667 0.00 0.00 0.00 4.61
414 435 2.402572 GCCCGAAGAAGCTTGAGCC 61.403 63.158 2.10 0.00 43.38 4.70
573 605 2.130395 CATCATCATCACCGTCCTTCG 58.870 52.381 0.00 0.00 39.52 3.79
615 659 7.879070 ACGAAAACAGAGTTCACACTACTATA 58.121 34.615 0.00 0.00 31.22 1.31
619 675 6.639686 TCATACGAAAACAGAGTTCACACTAC 59.360 38.462 0.00 0.00 31.22 2.73
734 794 1.876497 TTACTGTACCACCGACGGGC 61.876 60.000 20.00 3.43 36.48 6.13
735 795 0.602562 TTTACTGTACCACCGACGGG 59.397 55.000 20.00 7.12 40.11 5.28
740 800 8.323140 CGATAAACTAAATTTACTGTACCACCG 58.677 37.037 0.00 0.00 35.57 4.94
741 801 8.118607 GCGATAAACTAAATTTACTGTACCACC 58.881 37.037 0.00 0.00 35.57 4.61
742 802 7.842721 CGCGATAAACTAAATTTACTGTACCAC 59.157 37.037 0.00 0.00 35.57 4.16
743 803 7.545265 ACGCGATAAACTAAATTTACTGTACCA 59.455 33.333 15.93 0.00 35.57 3.25
767 828 1.613270 GCCGTCCTGCAAATTTTACG 58.387 50.000 0.00 0.00 0.00 3.18
768 829 1.613270 CGCCGTCCTGCAAATTTTAC 58.387 50.000 0.00 0.00 0.00 2.01
793 854 2.353208 GCTCTAATAGGCCAGTCATCCG 60.353 54.545 5.01 0.00 0.00 4.18
827 969 3.005472 GGTGTTGGGCTCTAAGTTTTTCC 59.995 47.826 0.00 0.00 0.00 3.13
836 978 1.904771 CGGATGGTGTTGGGCTCTA 59.095 57.895 0.00 0.00 0.00 2.43
873 1015 3.941188 CTGGACACGTGGCAGGGT 61.941 66.667 25.47 0.00 0.00 4.34
958 1106 2.290960 CGGAGGAAATGAAAGGGGAACT 60.291 50.000 0.00 0.00 0.00 3.01
1114 1275 5.919272 AACACGCATCTGATTCTCATATG 57.081 39.130 0.00 0.00 35.03 1.78
1144 1305 6.421485 ACTAACTCTATAGAAGTTCCGGTGA 58.579 40.000 16.13 0.00 0.00 4.02
1191 1352 1.807142 GGTCCTTAGCACAGAACAAGC 59.193 52.381 0.00 0.00 0.00 4.01
1293 1454 7.399191 ACTCAGTTACTCTGACCATACCATAAA 59.601 37.037 0.00 0.00 46.77 1.40
1376 1543 9.944663 GTTCATAAAAATACGAGCAATTGGATA 57.055 29.630 7.72 0.00 0.00 2.59
1396 1563 4.137116 ACAAGCGCTCCATAAGTTCATA 57.863 40.909 12.06 0.00 0.00 2.15
1501 1670 5.067805 AGCAAGTAAAACTCCCAGAAAACAG 59.932 40.000 0.00 0.00 0.00 3.16
1507 1676 4.141482 ACAGAAGCAAGTAAAACTCCCAGA 60.141 41.667 0.00 0.00 0.00 3.86
1511 1680 5.297029 ACAGAACAGAAGCAAGTAAAACTCC 59.703 40.000 0.00 0.00 0.00 3.85
1717 1886 8.681486 TCCAGATGTGATTATTCAACCATAAG 57.319 34.615 0.00 0.00 32.48 1.73
1721 1890 4.883585 GCTCCAGATGTGATTATTCAACCA 59.116 41.667 0.00 0.00 32.48 3.67
1733 1902 3.947910 AAATTTGGTGCTCCAGATGTG 57.052 42.857 11.24 0.00 45.22 3.21
1751 1920 7.119262 GCTACCTATGCTCAACTACTTCAAAAA 59.881 37.037 0.00 0.00 0.00 1.94
1762 1932 3.493524 GGGAGAAGCTACCTATGCTCAAC 60.494 52.174 0.00 0.00 40.22 3.18
1764 1934 2.320781 GGGAGAAGCTACCTATGCTCA 58.679 52.381 0.00 0.00 40.22 4.26
1774 1944 4.780021 AGAGATGAAAACTGGGAGAAGCTA 59.220 41.667 0.00 0.00 0.00 3.32
1823 1993 6.651225 AGAACAACAAATGAAGTAGGCTACTC 59.349 38.462 26.39 19.02 38.26 2.59
1832 2002 8.621532 TTGAGCTATAGAACAACAAATGAAGT 57.378 30.769 3.21 0.00 0.00 3.01
1833 2003 7.695618 GCTTGAGCTATAGAACAACAAATGAAG 59.304 37.037 3.21 0.00 38.21 3.02
1957 2298 4.163458 GGAATATGACCTCCACCACTTGTA 59.837 45.833 0.00 0.00 0.00 2.41
2189 2530 1.289160 CAGTCAAGAATCCTCCCCCA 58.711 55.000 0.00 0.00 0.00 4.96
2301 2642 0.954452 CCCTTTCTGAGGTTGCACAC 59.046 55.000 0.00 0.00 44.71 3.82
2337 2678 6.152932 AGGCAGAGCATTGTTAATTAATGG 57.847 37.500 0.31 0.00 36.33 3.16
2374 2717 2.353307 CGGCAGGACACTACATGTTGTA 60.353 50.000 12.62 0.00 43.56 2.41
2382 2725 2.094762 ACATTTCGGCAGGACACTAC 57.905 50.000 0.00 0.00 0.00 2.73
2389 2732 1.482593 AGAGGAGTACATTTCGGCAGG 59.517 52.381 0.00 0.00 0.00 4.85
2392 2735 2.674796 ACAGAGGAGTACATTTCGGC 57.325 50.000 0.00 0.00 0.00 5.54
2398 2741 6.875972 ACATTTAGGAACAGAGGAGTACAT 57.124 37.500 0.00 0.00 0.00 2.29
2399 2742 7.578955 GCTTACATTTAGGAACAGAGGAGTACA 60.579 40.741 0.00 0.00 0.00 2.90
2400 2743 6.757478 GCTTACATTTAGGAACAGAGGAGTAC 59.243 42.308 0.00 0.00 0.00 2.73
2401 2744 6.127140 GGCTTACATTTAGGAACAGAGGAGTA 60.127 42.308 0.00 0.00 0.00 2.59
2403 2746 5.104735 AGGCTTACATTTAGGAACAGAGGAG 60.105 44.000 0.00 0.00 0.00 3.69
2404 2747 4.783227 AGGCTTACATTTAGGAACAGAGGA 59.217 41.667 0.00 0.00 0.00 3.71
2406 2749 7.454260 AAAAGGCTTACATTTAGGAACAGAG 57.546 36.000 0.00 0.00 0.00 3.35
2407 2750 7.833285 AAAAAGGCTTACATTTAGGAACAGA 57.167 32.000 0.00 0.00 0.00 3.41
2408 2751 9.010029 TCTAAAAAGGCTTACATTTAGGAACAG 57.990 33.333 21.19 6.14 36.48 3.16
2409 2752 8.927675 TCTAAAAAGGCTTACATTTAGGAACA 57.072 30.769 21.19 7.21 36.48 3.18
2410 2753 9.227777 TCTCTAAAAAGGCTTACATTTAGGAAC 57.772 33.333 21.19 0.00 36.48 3.62
2411 2754 9.975218 ATCTCTAAAAAGGCTTACATTTAGGAA 57.025 29.630 21.19 13.95 36.48 3.36
2415 2758 9.747898 TGGAATCTCTAAAAAGGCTTACATTTA 57.252 29.630 0.00 1.24 0.00 1.40
2416 2759 8.650143 TGGAATCTCTAAAAAGGCTTACATTT 57.350 30.769 0.00 0.00 0.00 2.32
2418 2761 8.829373 ATTGGAATCTCTAAAAAGGCTTACAT 57.171 30.769 0.00 0.00 0.00 2.29
2419 2762 9.174166 GTATTGGAATCTCTAAAAAGGCTTACA 57.826 33.333 0.00 0.00 0.00 2.41
2420 2763 9.174166 TGTATTGGAATCTCTAAAAAGGCTTAC 57.826 33.333 0.00 0.00 0.00 2.34
2421 2764 9.396022 CTGTATTGGAATCTCTAAAAAGGCTTA 57.604 33.333 0.00 0.00 0.00 3.09
2424 2767 7.554476 AGTCTGTATTGGAATCTCTAAAAAGGC 59.446 37.037 0.00 0.00 0.00 4.35
2431 2774 9.000486 CGTATGTAGTCTGTATTGGAATCTCTA 58.000 37.037 0.00 0.00 0.00 2.43
2433 2776 7.040617 TCCGTATGTAGTCTGTATTGGAATCTC 60.041 40.741 0.00 0.00 0.00 2.75
2434 2777 6.776116 TCCGTATGTAGTCTGTATTGGAATCT 59.224 38.462 0.00 0.00 0.00 2.40
2435 2778 6.978338 TCCGTATGTAGTCTGTATTGGAATC 58.022 40.000 0.00 0.00 0.00 2.52
2436 2779 6.516860 GCTCCGTATGTAGTCTGTATTGGAAT 60.517 42.308 0.00 0.00 0.00 3.01
2437 2780 5.221185 GCTCCGTATGTAGTCTGTATTGGAA 60.221 44.000 0.00 0.00 0.00 3.53
2438 2781 4.277672 GCTCCGTATGTAGTCTGTATTGGA 59.722 45.833 0.00 0.00 0.00 3.53
2440 2783 5.183014 TGCTCCGTATGTAGTCTGTATTG 57.817 43.478 0.00 0.00 0.00 1.90
2441 2784 5.847111 TTGCTCCGTATGTAGTCTGTATT 57.153 39.130 0.00 0.00 0.00 1.89
2442 2785 5.847111 TTTGCTCCGTATGTAGTCTGTAT 57.153 39.130 0.00 0.00 0.00 2.29
2445 2788 5.109210 TCATTTTGCTCCGTATGTAGTCTG 58.891 41.667 0.00 0.00 0.00 3.51
2446 2789 5.105310 ACTCATTTTGCTCCGTATGTAGTCT 60.105 40.000 0.00 0.00 0.00 3.24
2447 2790 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2448 2791 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2449 2792 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2450 2793 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2451 2794 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2452 2795 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2453 2796 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2454 2797 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2455 2798 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2456 2799 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2457 2800 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2458 2801 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2469 2812 8.485976 AGAAGCATTTTAGAGTGTAGATTCAC 57.514 34.615 0.00 0.00 38.46 3.18
2529 2872 9.392259 CCTTCCGTTTCTAAATATAAGACCTTT 57.608 33.333 0.00 0.00 0.00 3.11
2530 2873 8.765517 TCCTTCCGTTTCTAAATATAAGACCTT 58.234 33.333 0.00 0.00 0.00 3.50
2531 2874 8.202811 GTCCTTCCGTTTCTAAATATAAGACCT 58.797 37.037 0.00 0.00 0.00 3.85
2532 2875 8.202811 AGTCCTTCCGTTTCTAAATATAAGACC 58.797 37.037 0.00 0.00 0.00 3.85
2537 2880 9.485206 GCATTAGTCCTTCCGTTTCTAAATATA 57.515 33.333 0.00 0.00 0.00 0.86
2538 2881 8.211629 AGCATTAGTCCTTCCGTTTCTAAATAT 58.788 33.333 0.00 0.00 0.00 1.28
2539 2882 7.494625 CAGCATTAGTCCTTCCGTTTCTAAATA 59.505 37.037 0.00 0.00 0.00 1.40
2540 2883 6.316390 CAGCATTAGTCCTTCCGTTTCTAAAT 59.684 38.462 0.00 0.00 0.00 1.40
2541 2884 5.642063 CAGCATTAGTCCTTCCGTTTCTAAA 59.358 40.000 0.00 0.00 0.00 1.85
2542 2885 5.046878 TCAGCATTAGTCCTTCCGTTTCTAA 60.047 40.000 0.00 0.00 0.00 2.10
2543 2886 4.464951 TCAGCATTAGTCCTTCCGTTTCTA 59.535 41.667 0.00 0.00 0.00 2.10
2544 2887 3.260884 TCAGCATTAGTCCTTCCGTTTCT 59.739 43.478 0.00 0.00 0.00 2.52
2545 2888 3.596214 TCAGCATTAGTCCTTCCGTTTC 58.404 45.455 0.00 0.00 0.00 2.78
2546 2889 3.695830 TCAGCATTAGTCCTTCCGTTT 57.304 42.857 0.00 0.00 0.00 3.60
2547 2890 3.695830 TTCAGCATTAGTCCTTCCGTT 57.304 42.857 0.00 0.00 0.00 4.44
2548 2891 3.008049 AGTTTCAGCATTAGTCCTTCCGT 59.992 43.478 0.00 0.00 0.00 4.69
2549 2892 3.600388 AGTTTCAGCATTAGTCCTTCCG 58.400 45.455 0.00 0.00 0.00 4.30
2550 2893 4.837972 AGAGTTTCAGCATTAGTCCTTCC 58.162 43.478 0.00 0.00 0.00 3.46
2551 2894 7.412020 CGTTAAGAGTTTCAGCATTAGTCCTTC 60.412 40.741 0.00 0.00 0.00 3.46
2552 2895 6.369065 CGTTAAGAGTTTCAGCATTAGTCCTT 59.631 38.462 0.00 0.00 0.00 3.36
2553 2896 5.869888 CGTTAAGAGTTTCAGCATTAGTCCT 59.130 40.000 0.00 0.00 0.00 3.85
2554 2897 5.867716 TCGTTAAGAGTTTCAGCATTAGTCC 59.132 40.000 0.00 0.00 0.00 3.85
2555 2898 6.946229 TCGTTAAGAGTTTCAGCATTAGTC 57.054 37.500 0.00 0.00 0.00 2.59
2556 2899 6.128526 GCTTCGTTAAGAGTTTCAGCATTAGT 60.129 38.462 0.00 0.00 34.37 2.24
2557 2900 6.128553 TGCTTCGTTAAGAGTTTCAGCATTAG 60.129 38.462 0.00 0.00 34.03 1.73
2558 2901 5.699001 TGCTTCGTTAAGAGTTTCAGCATTA 59.301 36.000 0.00 0.00 34.03 1.90
2559 2902 4.515191 TGCTTCGTTAAGAGTTTCAGCATT 59.485 37.500 0.00 0.00 34.03 3.56
2560 2903 4.065088 TGCTTCGTTAAGAGTTTCAGCAT 58.935 39.130 0.00 0.00 34.03 3.79
2561 2904 3.462982 TGCTTCGTTAAGAGTTTCAGCA 58.537 40.909 0.00 0.00 35.90 4.41
2562 2905 4.152402 TCATGCTTCGTTAAGAGTTTCAGC 59.848 41.667 0.00 0.00 34.37 4.26
2566 2909 4.455533 TGCATCATGCTTCGTTAAGAGTTT 59.544 37.500 11.84 0.00 45.31 2.66
2577 2920 6.369059 ACATAGTAACTTGCATCATGCTTC 57.631 37.500 11.84 0.00 45.31 3.86
2652 2996 8.950007 TCCCATTCCTATTTTTCTGTACTTTT 57.050 30.769 0.00 0.00 0.00 2.27
2653 2997 8.950007 TTCCCATTCCTATTTTTCTGTACTTT 57.050 30.769 0.00 0.00 0.00 2.66
2663 3007 4.540715 CTGCTCCTTCCCATTCCTATTTT 58.459 43.478 0.00 0.00 0.00 1.82
2690 3034 1.912001 CCACAACAGTGCACAAGTTG 58.088 50.000 34.41 34.41 45.97 3.16
2691 3035 0.173255 GCCACAACAGTGCACAAGTT 59.827 50.000 21.04 19.51 31.87 2.66
2740 3084 2.583520 CTCCCTCTCTGCTGTGGC 59.416 66.667 0.00 0.00 39.26 5.01
2743 3087 0.617249 CTTCCCTCCCTCTCTGCTGT 60.617 60.000 0.00 0.00 0.00 4.40
2746 3090 0.618968 TTCCTTCCCTCCCTCTCTGC 60.619 60.000 0.00 0.00 0.00 4.26
2747 3091 1.199615 GTTCCTTCCCTCCCTCTCTG 58.800 60.000 0.00 0.00 0.00 3.35
2754 3098 0.034089 CACCCATGTTCCTTCCCTCC 60.034 60.000 0.00 0.00 0.00 4.30
2810 3154 0.182061 ACCTGGTACGCGAGGAGATA 59.818 55.000 15.93 0.00 42.42 1.98
2819 3163 1.463444 CTTACTTGCAACCTGGTACGC 59.537 52.381 12.85 12.85 0.00 4.42
2821 3165 3.188667 GCTTCTTACTTGCAACCTGGTAC 59.811 47.826 0.00 0.00 0.00 3.34
2843 3187 5.947228 TGGATTCTAGCTTTTGTTCACTG 57.053 39.130 0.00 0.00 0.00 3.66
2845 3189 6.319141 AGTTGGATTCTAGCTTTTGTTCAC 57.681 37.500 0.00 0.00 0.00 3.18
2922 3298 2.033372 GACTAGGACTCCTTAGCCCAC 58.967 57.143 1.94 0.00 34.61 4.61
2928 3304 7.017452 GGATTACTAGAGGACTAGGACTCCTTA 59.983 44.444 14.55 2.66 46.85 2.69
2930 3306 5.311385 GGATTACTAGAGGACTAGGACTCCT 59.689 48.000 14.55 2.31 46.85 3.69
2977 3358 1.135689 CAAGCGTTAACCTGGCATCAC 60.136 52.381 0.00 0.00 0.00 3.06
2987 3368 0.517316 CCTGTCTGCCAAGCGTTAAC 59.483 55.000 0.00 0.00 0.00 2.01
2988 3369 0.107831 ACCTGTCTGCCAAGCGTTAA 59.892 50.000 0.00 0.00 0.00 2.01
3021 3402 3.736224 CATGGAGCCAGGGCCACT 61.736 66.667 6.18 0.00 43.17 4.00
3044 3425 6.769512 AGAACAAGCCAAGTAGATAACAGAA 58.230 36.000 0.00 0.00 0.00 3.02
3060 3441 7.166473 CGATGGAAAATTGCTAATAGAACAAGC 59.834 37.037 0.00 0.00 36.77 4.01
3072 3459 2.025887 AGTCCTCCGATGGAAAATTGCT 60.026 45.455 0.00 0.00 37.93 3.91
3088 3475 9.281371 GAGGTTAAGTTGTTAATAAACAGTCCT 57.719 33.333 6.73 7.66 45.99 3.85
3103 3490 6.936279 TGATCTACTCAAGGAGGTTAAGTTG 58.064 40.000 0.00 0.00 33.35 3.16
3109 3496 3.445008 TGCTGATCTACTCAAGGAGGTT 58.555 45.455 0.00 0.00 33.35 3.50
3182 3569 1.444895 GCACTTTGGATGCCTTGCG 60.445 57.895 0.00 0.00 37.08 4.85
3190 3577 1.187567 GGCCTTGGTGCACTTTGGAT 61.188 55.000 17.98 0.00 0.00 3.41
3200 3587 0.960364 AGCATTACGTGGCCTTGGTG 60.960 55.000 3.32 0.00 0.00 4.17
3249 3636 4.338879 AGATGAACTACTGCATTTGGCTT 58.661 39.130 0.00 0.00 45.15 4.35
3263 3650 7.782168 TCACATATAGAAGTCAGGAGATGAACT 59.218 37.037 0.00 0.00 40.43 3.01
3265 3652 8.539117 TTCACATATAGAAGTCAGGAGATGAA 57.461 34.615 0.00 0.00 40.43 2.57
3266 3653 8.539117 TTTCACATATAGAAGTCAGGAGATGA 57.461 34.615 0.00 0.00 34.79 2.92
3267 3654 8.637099 TCTTTCACATATAGAAGTCAGGAGATG 58.363 37.037 0.00 0.00 0.00 2.90
3268 3655 8.774546 TCTTTCACATATAGAAGTCAGGAGAT 57.225 34.615 0.00 0.00 0.00 2.75
3269 3656 8.774546 ATCTTTCACATATAGAAGTCAGGAGA 57.225 34.615 0.00 0.00 0.00 3.71
3410 3805 3.414700 GCCGGTGACACGCTTCAG 61.415 66.667 1.90 0.00 0.00 3.02
3541 3936 6.127479 TGAGAGTACAAAGTGCAAACCAAAAT 60.127 34.615 0.00 0.00 0.00 1.82
3542 3937 5.184096 TGAGAGTACAAAGTGCAAACCAAAA 59.816 36.000 0.00 0.00 0.00 2.44
3548 3943 6.449635 ACATTTGAGAGTACAAAGTGCAAA 57.550 33.333 0.00 0.00 41.87 3.68
3551 3946 6.539649 TGTACATTTGAGAGTACAAAGTGC 57.460 37.500 3.20 0.00 45.30 4.40
3557 3952 9.772973 ACATTAACTTGTACATTTGAGAGTACA 57.227 29.630 0.00 0.00 46.24 2.90
3611 4006 9.202273 GCATAGACCATGTAAAAATTGTTTTCA 57.798 29.630 0.00 0.00 35.50 2.69
3612 4007 9.423061 AGCATAGACCATGTAAAAATTGTTTTC 57.577 29.630 0.00 0.00 35.50 2.29
3633 4028 5.869649 TTCATACTTCCAGCACTAGCATA 57.130 39.130 0.00 0.00 45.49 3.14
3774 4169 5.448654 TCCAAAACTCCATTATCATCCAGG 58.551 41.667 0.00 0.00 0.00 4.45
3844 4239 3.126001 ACCCACGCGATATGATCATTT 57.874 42.857 15.93 5.85 0.00 2.32
3923 4318 6.601613 AGGTTCATTGTTGACTACACTTTTCA 59.398 34.615 0.00 0.00 36.21 2.69
3925 4320 7.093945 ACAAGGTTCATTGTTGACTACACTTTT 60.094 33.333 0.00 0.00 40.47 2.27
3979 4374 2.676471 ACCCATCAGTTTGCCCGC 60.676 61.111 0.00 0.00 0.00 6.13
4021 4416 6.072112 ACGAACTACTTGCAATCATTTTGT 57.928 33.333 0.00 0.00 0.00 2.83
4071 4471 5.006455 CAGAGCATACAGAACTACAGCAATG 59.994 44.000 0.00 0.00 0.00 2.82
4147 4547 4.202305 GCCACTCAGCTATTTAGATCACCT 60.202 45.833 0.00 0.00 0.00 4.00
4181 4581 6.700520 GTGGTACTAGTACACAATAGATTGGC 59.299 42.308 29.38 11.45 37.78 4.52
4182 4582 8.008513 AGTGGTACTAGTACACAATAGATTGG 57.991 38.462 29.38 0.00 37.78 3.16
4189 4589 7.562454 TGCCTATTAGTGGTACTAGTACACAAT 59.438 37.037 29.38 24.30 37.78 2.71
4262 4672 6.159575 TGGAATTTCTAGTTGATACCATCCCA 59.840 38.462 0.00 0.00 0.00 4.37
4307 4717 6.756299 TTGCAGCAATACATCTTGAATACA 57.244 33.333 2.83 0.00 0.00 2.29
4334 4744 3.119209 TCATGCAACAACAGAGTTTGCAA 60.119 39.130 11.84 0.00 38.25 4.08
4402 4812 3.931907 TCCTATGCCACACAGCTATTT 57.068 42.857 0.00 0.00 0.00 1.40
4465 4875 3.123621 AGCATCGTTCTCATTCGTTTCAC 59.876 43.478 0.00 0.00 0.00 3.18
4494 4904 7.099764 CACCAATACTGAAGTCTAGATGTTGT 58.900 38.462 0.00 0.00 0.00 3.32
4553 4963 4.258543 GTCCATTTCACCGGAGTTTCATA 58.741 43.478 9.46 0.00 29.98 2.15
4583 4993 4.581824 TGCAAAATAGAATCCAGCTCATCC 59.418 41.667 0.00 0.00 0.00 3.51
4590 5000 8.922676 GCAAATCATATGCAAAATAGAATCCAG 58.077 33.333 0.00 0.00 43.29 3.86
4630 5040 4.421058 TGTATGAAGCAACACTAGCTACG 58.579 43.478 0.00 0.00 42.53 3.51
4713 5124 5.856126 TGAAGTGACATTACATTTCGACC 57.144 39.130 0.00 0.00 38.65 4.79
4716 5127 9.034544 TCTATGATGAAGTGACATTACATTTCG 57.965 33.333 0.00 0.00 38.65 3.46
4758 5169 9.199982 AGCATACTCAACAGATTTTTCAATTTG 57.800 29.630 0.00 0.00 31.95 2.32
4773 5184 4.392921 TCTAGAAGCCAGCATACTCAAC 57.607 45.455 0.00 0.00 0.00 3.18
4778 5189 2.873649 GCCCATCTAGAAGCCAGCATAC 60.874 54.545 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.