Multiple sequence alignment - TraesCS2B01G515500

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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 TraesCS2B01G515500 chr2B 100.000 5268 0 0 1 5268 710285986 710280719 0.000000e+00 9729.0
1 TraesCS2B01G515500 chr2B 97.297 37 1 0 1162 1198 8325083 8325119 4.400000e-06 63.9
2 TraesCS2B01G515500 chr2D 90.909 2728 136 54 2589 5268 587699341 587696678 0.000000e+00 3561.0
3 TraesCS2B01G515500 chr2D 89.381 1695 79 39 1 1644 587701930 587700286 0.000000e+00 2039.0
4 TraesCS2B01G515500 chr2D 85.442 838 91 18 1648 2472 587700162 587699343 0.000000e+00 843.0
5 TraesCS2B01G515500 chr2D 86.928 153 13 6 2472 2622 122863518 122863371 1.170000e-36 165.0
6 TraesCS2B01G515500 chr2A 91.062 1723 94 26 3530 5218 722520337 722518641 0.000000e+00 2274.0
7 TraesCS2B01G515500 chr2A 90.209 1726 109 32 780 2472 722523019 722521321 0.000000e+00 2196.0
8 TraesCS2B01G515500 chr2A 93.545 1007 41 11 2589 3584 722521319 722520326 0.000000e+00 1478.0
9 TraesCS2B01G515500 chr2A 90.832 589 36 10 1 575 722523795 722523211 0.000000e+00 773.0
10 TraesCS2B01G515500 chr2A 91.753 194 12 4 4960 5151 32974343 32974152 3.130000e-67 267.0
11 TraesCS2B01G515500 chr4D 87.794 934 52 28 4373 5268 344372799 344373708 0.000000e+00 1037.0
12 TraesCS2B01G515500 chr3A 85.619 751 38 28 4560 5268 195451516 195452238 0.000000e+00 725.0
13 TraesCS2B01G515500 chr3A 92.308 182 11 2 4373 4554 195447429 195447607 6.770000e-64 255.0
14 TraesCS2B01G515500 chr3A 95.000 120 6 0 2471 2590 749204898 749205017 6.960000e-44 189.0
15 TraesCS2B01G515500 chr7B 78.649 370 68 6 1797 2164 611719008 611718648 8.820000e-58 235.0
16 TraesCS2B01G515500 chr7B 96.032 126 4 1 2473 2598 630887857 630887981 2.490000e-48 204.0
17 TraesCS2B01G515500 chr7B 96.581 117 4 0 2473 2589 679795727 679795611 1.500000e-45 195.0
18 TraesCS2B01G515500 chr1D 93.377 151 8 1 4373 4523 2480514 2480366 6.870000e-54 222.0
19 TraesCS2B01G515500 chr7D 96.581 117 4 0 2473 2589 93126729 93126845 1.500000e-45 195.0
20 TraesCS2B01G515500 chr7D 87.324 142 17 1 2472 2613 4241701 4241841 1.520000e-35 161.0
21 TraesCS2B01G515500 chr7D 74.495 396 69 15 1795 2164 562121360 562120971 5.500000e-30 143.0
22 TraesCS2B01G515500 chr6B 94.017 117 7 0 2473 2589 597021407 597021291 1.510000e-40 178.0
23 TraesCS2B01G515500 chr6B 87.931 116 8 5 1150 1262 424292566 424292678 1.190000e-26 132.0
24 TraesCS2B01G515500 chr5B 93.220 118 8 0 2472 2589 596547781 596547664 1.950000e-39 174.0
25 TraesCS2B01G515500 chr3B 93.220 118 7 1 2472 2589 532196372 532196256 7.010000e-39 172.0


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 TraesCS2B01G515500 chr2B 710280719 710285986 5267 True 9729.000000 9729 100.000000 1 5268 1 chr2B.!!$R1 5267
1 TraesCS2B01G515500 chr2D 587696678 587701930 5252 True 2147.666667 3561 88.577333 1 5268 3 chr2D.!!$R2 5267
2 TraesCS2B01G515500 chr2A 722518641 722523795 5154 True 1680.250000 2274 91.412000 1 5218 4 chr2A.!!$R2 5217
3 TraesCS2B01G515500 chr4D 344372799 344373708 909 False 1037.000000 1037 87.794000 4373 5268 1 chr4D.!!$F1 895
4 TraesCS2B01G515500 chr3A 195447429 195452238 4809 False 490.000000 725 88.963500 4373 5268 2 chr3A.!!$F2 895

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
954 1027 0.028770 CCACGACATCTCGAGCTCTC 59.971 60.0 12.85 0.0 43.06 3.20 F
2491 2736 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.0 5.23 0.0 44.66 2.17 F
2492 2737 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.0 5.23 0.0 44.66 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2472 2717 0.032813 AATTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.0 46.06 2.59 R
4159 4472 0.106335 CTCCAGCAGCATCTCGGATT 59.894 55.0 0.00 0.0 0.00 3.01 R
4458 4771 0.248784 TCATCGCATCTGACTGCTCG 60.249 55.0 9.33 0.0 40.06 5.03 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
110 111 4.697756 CGAAGAACCCTGCCGGCA 62.698 66.667 30.59 30.59 33.26 5.69
288 289 4.451150 TGCCGCCGTCTGATGACC 62.451 66.667 0.00 0.00 39.94 4.02
314 315 4.933064 GCGGTGGATCCTCGCTCG 62.933 72.222 31.27 20.21 45.16 5.03
345 346 4.328440 GCTGCTACTGTGACTATTCTGTTG 59.672 45.833 0.00 0.00 0.00 3.33
554 570 0.664761 CCAGTTGTGTTGACAGCAGG 59.335 55.000 0.00 0.00 35.83 4.85
558 574 0.254462 TTGTGTTGACAGCAGGTGGA 59.746 50.000 4.26 0.00 32.26 4.02
561 577 0.320683 TGTTGACAGCAGGTGGATCG 60.321 55.000 4.26 0.00 0.00 3.69
576 592 4.433615 GTGGATCGCTGATTTCTCTGTTA 58.566 43.478 0.00 0.00 0.00 2.41
579 595 6.701841 GTGGATCGCTGATTTCTCTGTTAATA 59.298 38.462 0.00 0.00 0.00 0.98
582 598 7.115663 GGATCGCTGATTTCTCTGTTAATACTC 59.884 40.741 0.00 0.00 0.00 2.59
615 631 8.646900 TGTTCTATGATGCTACATAATACACCA 58.353 33.333 5.32 0.00 33.26 4.17
677 702 8.792830 TTTTCCAGGTCTATAACTTCTCAATG 57.207 34.615 0.00 0.00 0.00 2.82
725 750 7.524717 AAACAGCAAACTCTACCATACAAAT 57.475 32.000 0.00 0.00 0.00 2.32
727 752 7.145932 ACAGCAAACTCTACCATACAAATTC 57.854 36.000 0.00 0.00 0.00 2.17
728 753 6.714810 ACAGCAAACTCTACCATACAAATTCA 59.285 34.615 0.00 0.00 0.00 2.57
730 755 7.912250 CAGCAAACTCTACCATACAAATTCATC 59.088 37.037 0.00 0.00 0.00 2.92
731 756 7.611467 AGCAAACTCTACCATACAAATTCATCA 59.389 33.333 0.00 0.00 0.00 3.07
866 926 0.832983 TACACGTGGGGCCAGTTACT 60.833 55.000 21.57 0.00 0.00 2.24
870 930 0.974010 CGTGGGGCCAGTTACTCCTA 60.974 60.000 4.39 0.00 0.00 2.94
878 938 1.815003 CCAGTTACTCCTACGACGGTT 59.185 52.381 0.00 0.00 0.00 4.44
954 1027 0.028770 CCACGACATCTCGAGCTCTC 59.971 60.000 12.85 0.00 43.06 3.20
1065 1138 4.803426 CTGCCCTCCGTCTGCGTC 62.803 72.222 0.00 0.00 36.15 5.19
1200 1285 3.003173 TCCGCCAAGGAGTCCCTG 61.003 66.667 5.25 2.53 45.98 4.45
1218 1303 3.764466 CTCCTCGCCGTGAGCCTT 61.764 66.667 3.22 0.00 43.82 4.35
1219 1304 3.708220 CTCCTCGCCGTGAGCCTTC 62.708 68.421 3.22 0.00 43.82 3.46
1220 1305 4.821589 CCTCGCCGTGAGCCTTCC 62.822 72.222 3.22 0.00 43.82 3.46
1224 1309 4.785453 GCCGTGAGCCTTCCCCTG 62.785 72.222 0.00 0.00 34.35 4.45
1330 1421 1.473257 GCCCAGTGCATCTGTCGATTA 60.473 52.381 13.06 0.00 42.19 1.75
1331 1422 2.905075 CCCAGTGCATCTGTCGATTAA 58.095 47.619 13.06 0.00 42.19 1.40
1342 1448 8.309656 TGCATCTGTCGATTAATCTCTCAATAT 58.690 33.333 13.45 4.38 0.00 1.28
1354 1460 4.529897 TCTCTCAATATGCCAATTGTGCT 58.470 39.130 16.52 7.74 37.94 4.40
1424 1530 1.709147 CCTCGATTTTGCAGAGCCCG 61.709 60.000 0.00 0.00 0.00 6.13
1431 1537 2.529454 TTTGCAGAGCCCGCCGAATA 62.529 55.000 0.00 0.00 0.00 1.75
1441 1547 1.798813 CCCGCCGAATAATGAGCTTAC 59.201 52.381 0.00 0.00 0.00 2.34
1442 1548 1.798813 CCGCCGAATAATGAGCTTACC 59.201 52.381 0.00 0.00 0.00 2.85
1449 1555 5.354234 CCGAATAATGAGCTTACCAGTGTTT 59.646 40.000 0.00 0.00 0.00 2.83
1488 1594 0.179004 TGGGTTCTGCATTCACGGTT 60.179 50.000 0.00 0.00 0.00 4.44
1787 2013 5.819901 GGAACTCCCATCATTTCTGACTAAG 59.180 44.000 0.00 0.00 33.22 2.18
1791 2017 6.157645 ACTCCCATCATTTCTGACTAAGACAT 59.842 38.462 0.00 0.00 33.46 3.06
1813 2049 2.754472 GGACATTTTGTTGGTCCTTGC 58.246 47.619 0.00 0.00 45.99 4.01
1830 2066 7.229306 TGGTCCTTGCTCATTAATCATATGTTC 59.771 37.037 1.90 0.00 0.00 3.18
1844 2080 6.908870 TCATATGTTCCACTTTTCAGATCG 57.091 37.500 1.90 0.00 0.00 3.69
1850 2086 2.093658 TCCACTTTTCAGATCGCCCTAC 60.094 50.000 0.00 0.00 0.00 3.18
1899 2135 1.043816 CGGTGATAGCAGTCCTGGAT 58.956 55.000 0.00 0.00 0.00 3.41
1928 2164 5.010922 TGCATCCAAGCTTTTGTTTGAGTAT 59.989 36.000 0.00 0.00 42.20 2.12
1987 2223 5.189180 ACTCACCATTTTAATCAGAGCTCC 58.811 41.667 10.93 0.00 0.00 4.70
1997 2233 3.922171 ATCAGAGCTCCCCTTACTTTG 57.078 47.619 10.93 0.00 0.00 2.77
2009 2245 5.046304 TCCCCTTACTTTGTTCTCATGAGAG 60.046 44.000 23.92 15.12 43.48 3.20
2010 2246 5.280215 CCCCTTACTTTGTTCTCATGAGAGT 60.280 44.000 23.92 19.59 42.66 3.24
2019 2255 5.461526 TGTTCTCATGAGAGTTGAGTTACG 58.538 41.667 23.92 0.00 42.66 3.18
2021 2257 6.206048 TGTTCTCATGAGAGTTGAGTTACGTA 59.794 38.462 23.92 3.29 42.66 3.57
2024 2260 6.092396 TCTCATGAGAGTTGAGTTACGTAGTC 59.908 42.308 21.67 0.00 41.29 2.59
2057 2293 7.815398 TTTATCATTAAATGCTGTGTTGCAG 57.185 32.000 0.00 0.00 46.71 4.41
2102 2339 8.408043 TCTTCCTTTGACAAAATGTGTATCAT 57.592 30.769 1.62 0.00 41.96 2.45
2202 2439 3.495331 TGGCTACTGCAAAATTTCCTCA 58.505 40.909 0.00 0.00 41.91 3.86
2217 2454 3.194005 TCCTCAAACGTCAAGCTCTTT 57.806 42.857 0.00 0.00 0.00 2.52
2233 2470 8.879759 TCAAGCTCTTTAATACGGTAATTTCAG 58.120 33.333 0.00 0.00 0.00 3.02
2242 2479 7.972832 AATACGGTAATTTCAGAAGTTGTGA 57.027 32.000 0.00 0.00 0.00 3.58
2249 2486 8.406297 GGTAATTTCAGAAGTTGTGAAAAGTCT 58.594 33.333 26.28 15.79 44.81 3.24
2259 2496 6.679327 GTTGTGAAAAGTCTCCTACAACTT 57.321 37.500 0.00 0.00 42.56 2.66
2274 2511 2.739379 ACAACTTTTGTGCGTTTTTGGG 59.261 40.909 0.00 0.00 43.48 4.12
2284 2521 4.226761 GTGCGTTTTTGGGTCTATCTTTG 58.773 43.478 0.00 0.00 0.00 2.77
2301 2538 5.689383 TCTTTGCAACTACCTCATGTTTC 57.311 39.130 0.00 0.00 0.00 2.78
2321 2558 6.204301 TGTTTCCAATGTTTGTGCCATTTATG 59.796 34.615 0.00 0.00 30.28 1.90
2327 2564 5.637006 TGTTTGTGCCATTTATGTACCTC 57.363 39.130 0.00 0.00 0.00 3.85
2341 2578 0.830648 TACCTCCCTACAGCATGCAC 59.169 55.000 21.98 0.00 42.53 4.57
2343 2580 0.182061 CCTCCCTACAGCATGCACAT 59.818 55.000 21.98 7.04 42.53 3.21
2352 2589 6.262944 CCCTACAGCATGCACATCTAATTTTA 59.737 38.462 21.98 0.00 42.53 1.52
2355 2592 9.740239 CTACAGCATGCACATCTAATTTTATTT 57.260 29.630 21.98 0.00 42.53 1.40
2381 2618 8.994429 TTTCAAAATGAAATTACAGTGTGTGT 57.006 26.923 5.88 0.00 41.02 3.72
2382 2619 8.627487 TTCAAAATGAAATTACAGTGTGTGTC 57.373 30.769 5.88 0.00 35.50 3.67
2383 2620 7.995289 TCAAAATGAAATTACAGTGTGTGTCT 58.005 30.769 5.88 0.00 40.94 3.41
2384 2621 8.465999 TCAAAATGAAATTACAGTGTGTGTCTT 58.534 29.630 5.88 0.00 40.94 3.01
2385 2622 8.745837 CAAAATGAAATTACAGTGTGTGTCTTC 58.254 33.333 5.88 2.69 40.94 2.87
2386 2623 6.560253 ATGAAATTACAGTGTGTGTCTTCC 57.440 37.500 5.88 0.00 40.94 3.46
2387 2624 5.680619 TGAAATTACAGTGTGTGTCTTCCT 58.319 37.500 5.88 0.00 40.94 3.36
2394 2631 5.057149 ACAGTGTGTGTCTTCCTTTATGAC 58.943 41.667 0.00 0.00 31.90 3.06
2395 2632 4.452455 CAGTGTGTGTCTTCCTTTATGACC 59.548 45.833 0.00 0.00 32.55 4.02
2396 2633 4.348168 AGTGTGTGTCTTCCTTTATGACCT 59.652 41.667 0.00 0.00 32.55 3.85
2411 2648 7.439655 CCTTTATGACCTGTAGCTCTTGTAATC 59.560 40.741 0.00 0.00 0.00 1.75
2414 2651 5.016831 TGACCTGTAGCTCTTGTAATCTGA 58.983 41.667 0.00 0.00 0.00 3.27
2443 2688 6.569127 TCCCAAGTTCATACTAAGGCATTA 57.431 37.500 0.00 0.00 33.17 1.90
2472 2717 6.294473 CAGCCATTTATCTGTCTTATCCAGT 58.706 40.000 0.00 0.00 0.00 4.00
2474 2719 7.386299 CAGCCATTTATCTGTCTTATCCAGTAC 59.614 40.741 0.00 0.00 0.00 2.73
2475 2720 7.291182 AGCCATTTATCTGTCTTATCCAGTACT 59.709 37.037 0.00 0.00 0.00 2.73
2476 2721 7.600752 GCCATTTATCTGTCTTATCCAGTACTC 59.399 40.741 0.00 0.00 0.00 2.59
2477 2722 8.091449 CCATTTATCTGTCTTATCCAGTACTCC 58.909 40.741 0.00 0.00 0.00 3.85
2478 2723 7.598759 TTTATCTGTCTTATCCAGTACTCCC 57.401 40.000 0.00 0.00 0.00 4.30
2479 2724 4.883021 TCTGTCTTATCCAGTACTCCCT 57.117 45.455 0.00 0.00 0.00 4.20
2481 2726 3.892588 CTGTCTTATCCAGTACTCCCTCC 59.107 52.174 0.00 0.00 0.00 4.30
2482 2727 2.885894 GTCTTATCCAGTACTCCCTCCG 59.114 54.545 0.00 0.00 0.00 4.63
2483 2728 2.512896 TCTTATCCAGTACTCCCTCCGT 59.487 50.000 0.00 0.00 0.00 4.69
2484 2729 2.653234 TATCCAGTACTCCCTCCGTC 57.347 55.000 0.00 0.00 0.00 4.79
2485 2730 0.106116 ATCCAGTACTCCCTCCGTCC 60.106 60.000 0.00 0.00 0.00 4.79
2486 2731 2.119655 CCAGTACTCCCTCCGTCCG 61.120 68.421 0.00 0.00 0.00 4.79
2487 2732 2.119655 CAGTACTCCCTCCGTCCGG 61.120 68.421 0.00 0.00 0.00 5.14
2488 2733 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
2489 2734 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2490 2735 0.754587 GTACTCCCTCCGTCCGGAAT 60.755 60.000 5.23 0.00 44.66 3.01
2491 2736 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
2492 2737 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
2493 2738 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
2494 2739 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
2495 2740 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
2496 2741 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2497 2742 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2498 2743 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2499 2744 1.135315 TCCGTCCGGAATTACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2500 2745 0.643820 CGTCCGGAATTACTTGTCGC 59.356 55.000 5.23 0.00 0.00 5.19
2501 2746 1.004595 GTCCGGAATTACTTGTCGCC 58.995 55.000 5.23 0.00 0.00 5.54
2502 2747 0.458889 TCCGGAATTACTTGTCGCCG 60.459 55.000 0.00 0.00 38.54 6.46
2503 2748 0.458889 CCGGAATTACTTGTCGCCGA 60.459 55.000 0.00 0.00 41.11 5.54
2504 2749 1.352114 CGGAATTACTTGTCGCCGAA 58.648 50.000 0.00 0.00 41.11 4.30
2505 2750 1.727880 CGGAATTACTTGTCGCCGAAA 59.272 47.619 0.00 0.00 41.11 3.46
2506 2751 2.350498 CGGAATTACTTGTCGCCGAAAT 59.650 45.455 0.00 0.00 41.11 2.17
2507 2752 3.680789 GGAATTACTTGTCGCCGAAATG 58.319 45.455 0.00 0.00 0.00 2.32
2508 2753 3.372822 GGAATTACTTGTCGCCGAAATGA 59.627 43.478 0.00 0.00 0.00 2.57
2509 2754 4.142773 GGAATTACTTGTCGCCGAAATGAA 60.143 41.667 0.00 0.00 0.00 2.57
2510 2755 5.448632 GGAATTACTTGTCGCCGAAATGAAT 60.449 40.000 0.00 0.00 0.00 2.57
2511 2756 6.238266 GGAATTACTTGTCGCCGAAATGAATA 60.238 38.462 0.00 0.00 0.00 1.75
2512 2757 6.671614 ATTACTTGTCGCCGAAATGAATAA 57.328 33.333 0.00 0.00 0.00 1.40
2513 2758 6.483385 TTACTTGTCGCCGAAATGAATAAA 57.517 33.333 0.00 0.00 0.00 1.40
2514 2759 5.365403 ACTTGTCGCCGAAATGAATAAAA 57.635 34.783 0.00 0.00 0.00 1.52
2515 2760 5.764131 ACTTGTCGCCGAAATGAATAAAAA 58.236 33.333 0.00 0.00 0.00 1.94
2516 2761 6.386654 ACTTGTCGCCGAAATGAATAAAAAT 58.613 32.000 0.00 0.00 0.00 1.82
2517 2762 6.307800 ACTTGTCGCCGAAATGAATAAAAATG 59.692 34.615 0.00 0.00 0.00 2.32
2518 2763 5.098893 TGTCGCCGAAATGAATAAAAATGG 58.901 37.500 0.00 0.00 0.00 3.16
2519 2764 5.106118 TGTCGCCGAAATGAATAAAAATGGA 60.106 36.000 0.00 0.00 0.00 3.41
2520 2765 5.977129 GTCGCCGAAATGAATAAAAATGGAT 59.023 36.000 0.00 0.00 0.00 3.41
2521 2766 5.976534 TCGCCGAAATGAATAAAAATGGATG 59.023 36.000 0.00 0.00 0.00 3.51
2522 2767 5.748152 CGCCGAAATGAATAAAAATGGATGT 59.252 36.000 0.00 0.00 0.00 3.06
2523 2768 6.915300 CGCCGAAATGAATAAAAATGGATGTA 59.085 34.615 0.00 0.00 0.00 2.29
2524 2769 7.594758 CGCCGAAATGAATAAAAATGGATGTAT 59.405 33.333 0.00 0.00 0.00 2.29
2525 2770 8.915654 GCCGAAATGAATAAAAATGGATGTATC 58.084 33.333 0.00 0.00 0.00 2.24
2554 2799 9.733556 AAAGTAAAACATGTCTACATACATCCA 57.266 29.630 16.34 0.00 38.01 3.41
2555 2800 9.905713 AAGTAAAACATGTCTACATACATCCAT 57.094 29.630 16.34 0.00 38.01 3.41
2556 2801 9.905713 AGTAAAACATGTCTACATACATCCATT 57.094 29.630 16.34 0.00 38.01 3.16
2559 2804 8.806429 AAACATGTCTACATACATCCATTTCA 57.194 30.769 0.00 0.00 38.01 2.69
2560 2805 8.985315 AACATGTCTACATACATCCATTTCAT 57.015 30.769 0.00 0.00 38.01 2.57
2561 2806 8.985315 ACATGTCTACATACATCCATTTCATT 57.015 30.769 0.00 0.00 38.01 2.57
2562 2807 8.843262 ACATGTCTACATACATCCATTTCATTG 58.157 33.333 0.00 0.00 38.01 2.82
2563 2808 9.059260 CATGTCTACATACATCCATTTCATTGA 57.941 33.333 0.00 0.00 38.01 2.57
2564 2809 8.437360 TGTCTACATACATCCATTTCATTGAC 57.563 34.615 0.00 0.00 0.00 3.18
2565 2810 8.046107 TGTCTACATACATCCATTTCATTGACA 58.954 33.333 0.00 0.00 0.00 3.58
2566 2811 8.892723 GTCTACATACATCCATTTCATTGACAA 58.107 33.333 0.00 0.00 0.00 3.18
2567 2812 9.112725 TCTACATACATCCATTTCATTGACAAG 57.887 33.333 0.00 0.00 0.00 3.16
2568 2813 7.707624 ACATACATCCATTTCATTGACAAGT 57.292 32.000 0.00 0.00 0.00 3.16
2569 2814 8.806429 ACATACATCCATTTCATTGACAAGTA 57.194 30.769 0.00 0.00 0.00 2.24
2570 2815 9.412460 ACATACATCCATTTCATTGACAAGTAT 57.588 29.630 0.00 0.00 0.00 2.12
2574 2819 8.253113 ACATCCATTTCATTGACAAGTATTTCC 58.747 33.333 0.00 0.00 0.00 3.13
2575 2820 6.851609 TCCATTTCATTGACAAGTATTTCCG 58.148 36.000 0.00 0.00 0.00 4.30
2576 2821 6.035843 CCATTTCATTGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 0.00 5.14
2577 2822 6.127758 CCATTTCATTGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 0.00 5.14
2578 2823 5.873179 TTCATTGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 0.00 4.79
2579 2824 3.930229 TCATTGACAAGTATTTCCGGACG 59.070 43.478 1.83 0.00 0.00 4.79
2580 2825 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2581 2826 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2582 2827 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2583 2828 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2584 2829 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2585 2830 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2586 2831 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2587 2832 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2588 2833 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2589 2834 0.682209 TTTCCGGACGGAGGGAGTAG 60.682 60.000 13.64 0.00 46.06 2.57
2590 2835 3.217743 CCGGACGGAGGGAGTAGC 61.218 72.222 4.40 0.00 37.50 3.58
2591 2836 2.124236 CGGACGGAGGGAGTAGCT 60.124 66.667 0.00 0.00 0.00 3.32
2592 2837 1.147824 CGGACGGAGGGAGTAGCTA 59.852 63.158 0.00 0.00 0.00 3.32
2593 2838 0.250814 CGGACGGAGGGAGTAGCTAT 60.251 60.000 0.00 0.00 0.00 2.97
2594 2839 1.002888 CGGACGGAGGGAGTAGCTATA 59.997 57.143 0.00 0.00 0.00 1.31
2595 2840 2.355920 CGGACGGAGGGAGTAGCTATAT 60.356 54.545 0.00 0.00 0.00 0.86
2631 2876 4.261322 CCATGTTGAGTTCTGTTGTTCCAG 60.261 45.833 0.00 0.00 0.00 3.86
2646 2895 1.729586 TCCAGGCCTCACAGTTTACT 58.270 50.000 0.00 0.00 0.00 2.24
2700 2949 3.491342 TGTTCTGACTACTCAGCTGTCT 58.509 45.455 14.67 2.22 43.45 3.41
2736 2985 2.761208 CAGGATGAAGGAGGAGTACGTT 59.239 50.000 0.00 0.00 39.69 3.99
2741 2990 1.477295 GAAGGAGGAGTACGTTGAGGG 59.523 57.143 0.00 0.00 0.00 4.30
2800 3049 3.486383 CCTGAACAACTGAAGGGCTTAA 58.514 45.455 0.00 0.00 0.00 1.85
2817 3066 3.614870 GCTTAATTGGACAAACTGCAGGG 60.615 47.826 19.93 9.69 0.00 4.45
2826 3075 0.771127 AAACTGCAGGGGCTCTACAA 59.229 50.000 19.93 0.00 41.91 2.41
2955 3206 6.046593 TCCAGTTTTATTAGGACATACTGCG 58.953 40.000 0.00 0.00 32.33 5.18
2962 3213 7.946655 TTATTAGGACATACTGCGAATTCAG 57.053 36.000 6.22 0.00 39.86 3.02
2968 3219 4.314961 ACATACTGCGAATTCAGACAACA 58.685 39.130 6.22 0.00 37.51 3.33
2973 3224 2.942376 TGCGAATTCAGACAACACAACT 59.058 40.909 6.22 0.00 0.00 3.16
2996 3247 6.599638 ACTGCAGGATTTATTACTGACCTTTC 59.400 38.462 19.93 0.00 34.21 2.62
2997 3248 6.721318 TGCAGGATTTATTACTGACCTTTCT 58.279 36.000 0.00 0.00 34.21 2.52
2999 3250 7.121168 TGCAGGATTTATTACTGACCTTTCTTG 59.879 37.037 0.00 0.00 34.21 3.02
3000 3251 7.121315 GCAGGATTTATTACTGACCTTTCTTGT 59.879 37.037 0.00 0.00 34.21 3.16
3012 3263 8.459635 ACTGACCTTTCTTGTTAAAAGAAACTC 58.540 33.333 6.24 5.30 40.25 3.01
3045 3296 7.916977 GCTTCAATGCATTTGTAATCACTGATA 59.083 33.333 9.83 0.00 36.65 2.15
3047 3298 9.955208 TTCAATGCATTTGTAATCACTGATATC 57.045 29.630 9.83 0.00 36.65 1.63
3269 3521 9.793252 GTTATGCTATTTTTCATTCTGTGATGT 57.207 29.630 0.00 0.00 36.54 3.06
3273 3525 8.525316 TGCTATTTTTCATTCTGTGATGTCATT 58.475 29.630 0.00 0.00 36.54 2.57
3619 3931 6.327154 TGTACCATATGTCTTAAGTGTCACG 58.673 40.000 1.63 0.00 0.00 4.35
3728 4040 6.958193 GTCAGAGAAAATAAAAGCTGATGACG 59.042 38.462 0.00 0.00 35.20 4.35
3865 4177 1.001633 TCCCGTAAGCAAGACCAGAAC 59.998 52.381 0.00 0.00 0.00 3.01
3866 4178 1.270625 CCCGTAAGCAAGACCAGAACA 60.271 52.381 0.00 0.00 0.00 3.18
4002 4314 2.545322 GCCTACCAATACAGTAGCGTCC 60.545 54.545 0.00 0.00 36.65 4.79
4003 4315 2.957006 CCTACCAATACAGTAGCGTCCT 59.043 50.000 0.00 0.00 36.65 3.85
4018 4330 2.417515 GCGTCCTTTCGATCCTCTCTTT 60.418 50.000 0.00 0.00 0.00 2.52
4026 4338 6.874134 CCTTTCGATCCTCTCTTTTAGACAAA 59.126 38.462 0.00 0.00 0.00 2.83
4032 4344 8.887717 CGATCCTCTCTTTTAGACAAATCAATT 58.112 33.333 0.00 0.00 0.00 2.32
4051 4363 9.439500 AATCAATTTAATCATGTTCCACAAAGG 57.561 29.630 0.00 0.00 39.47 3.11
4075 4388 5.514204 GCAGAATGAATGGTTTGAAATCTCG 59.486 40.000 0.00 0.00 39.69 4.04
4159 4472 8.593679 TGGTTGTTCTGTCTTCTCATTTAGATA 58.406 33.333 0.00 0.00 33.05 1.98
4219 4532 2.338620 GAAGGGCCGCAACCAAAC 59.661 61.111 0.00 0.00 0.00 2.93
4237 4550 2.046285 CCCAATGGAGAACACGCCC 61.046 63.158 0.00 0.00 0.00 6.13
4252 4565 0.939577 CGCCCGATGTAGTGATTCCG 60.940 60.000 0.00 0.00 0.00 4.30
4290 4603 1.847798 TTGGGCACTAACCGGAGCAT 61.848 55.000 9.46 0.00 0.00 3.79
4355 4668 3.270027 TCCAGGTTTTCGCATACATGAG 58.730 45.455 0.00 0.00 0.00 2.90
4436 4749 4.521256 GCTGGCTAGAGTAGTTACTGCTAT 59.479 45.833 2.37 2.64 36.50 2.97
4437 4750 5.706369 GCTGGCTAGAGTAGTTACTGCTATA 59.294 44.000 2.37 3.80 36.50 1.31
4458 4771 3.895232 TCCTGGAGTTGAGCAATACTC 57.105 47.619 0.00 0.00 46.45 2.59
4486 4799 5.680229 CAGTCAGATGCGATGAAAAATTAGC 59.320 40.000 0.00 0.00 0.00 3.09
4488 4801 5.680229 GTCAGATGCGATGAAAAATTAGCTG 59.320 40.000 0.00 0.00 0.00 4.24
4535 4848 8.739972 ACTCTGAACTGTAATTTGTTTTGTTCT 58.260 29.630 0.00 0.00 35.00 3.01
4601 8820 5.684626 CCAAAGTAAGTTAGCTCGGTATACG 59.315 44.000 0.00 0.00 46.11 3.06
4647 8866 4.723789 AGGAGGTAGAAATGTGGATCATGT 59.276 41.667 0.00 0.00 36.81 3.21
4684 8919 1.259142 TTTGGGCCGGTGATCTACGA 61.259 55.000 1.90 0.00 0.00 3.43
4692 8927 2.193447 CGGTGATCTACGACCATTGTG 58.807 52.381 3.97 0.00 31.97 3.33
4713 8951 5.534654 TGTGTCTAAAATCTTCCCCTTGTTG 59.465 40.000 0.00 0.00 0.00 3.33
4715 8953 5.163034 TGTCTAAAATCTTCCCCTTGTTGGA 60.163 40.000 0.00 0.00 38.35 3.53
4716 8954 5.952347 GTCTAAAATCTTCCCCTTGTTGGAT 59.048 40.000 0.00 0.00 38.35 3.41
4718 8956 5.488262 AAAATCTTCCCCTTGTTGGATTG 57.512 39.130 0.00 0.00 38.35 2.67
4719 8957 1.923356 TCTTCCCCTTGTTGGATTGC 58.077 50.000 0.00 0.00 38.35 3.56
4720 8958 1.146774 TCTTCCCCTTGTTGGATTGCA 59.853 47.619 0.00 0.00 38.35 4.08
4721 8959 2.181975 CTTCCCCTTGTTGGATTGCAT 58.818 47.619 0.00 0.00 38.35 3.96
4722 8960 1.851304 TCCCCTTGTTGGATTGCATC 58.149 50.000 0.00 0.00 38.35 3.91
4723 8961 1.076841 TCCCCTTGTTGGATTGCATCA 59.923 47.619 0.00 0.00 38.35 3.07
4724 8962 1.479323 CCCCTTGTTGGATTGCATCAG 59.521 52.381 0.00 0.00 38.35 2.90
4725 8963 1.479323 CCCTTGTTGGATTGCATCAGG 59.521 52.381 0.00 0.00 38.35 3.86
4726 8964 2.449464 CCTTGTTGGATTGCATCAGGA 58.551 47.619 0.00 0.00 38.35 3.86
4727 8965 2.426024 CCTTGTTGGATTGCATCAGGAG 59.574 50.000 0.00 0.00 38.35 3.69
4728 8966 2.885135 TGTTGGATTGCATCAGGAGT 57.115 45.000 0.00 0.00 0.00 3.85
4729 8967 3.998913 TGTTGGATTGCATCAGGAGTA 57.001 42.857 0.00 0.00 0.00 2.59
4730 8968 3.609853 TGTTGGATTGCATCAGGAGTAC 58.390 45.455 0.00 0.00 0.00 2.73
4763 9001 6.437477 TCATAGTATAAGCCGTCATTCCTCAT 59.563 38.462 0.00 0.00 0.00 2.90
4766 9004 6.010850 AGTATAAGCCGTCATTCCTCATAGA 58.989 40.000 0.00 0.00 0.00 1.98
4772 9018 2.474816 GTCATTCCTCATAGACGGCAC 58.525 52.381 0.00 0.00 0.00 5.01
4955 9226 3.056536 TCTTCCTTCATCGTCAGTTCAGG 60.057 47.826 0.00 0.00 0.00 3.86
4988 9261 1.133606 CACCTACCTCTCCCTCTCTCC 60.134 61.905 0.00 0.00 0.00 3.71
5023 9298 6.368805 AGTTCACCCAGAAGAGAAGAAAAAT 58.631 36.000 0.00 0.00 36.78 1.82
5065 9340 3.124921 GACACCCAATGCCGTCGG 61.125 66.667 6.99 6.99 0.00 4.79
5100 9380 1.303970 TGCCATTTCCATGTGCGGA 60.304 52.632 0.00 0.00 32.24 5.54
5153 9434 6.591935 TCAACAAACTGGAGAAGTAACAGAT 58.408 36.000 0.00 0.00 38.56 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
314 315 2.221981 GTCACAGTAGCAGCACAAGAAC 59.778 50.000 0.00 0.00 0.00 3.01
432 433 3.065925 ACAGCAAGAAAGTTCTGAAGCAC 59.934 43.478 12.84 0.00 37.65 4.40
554 570 2.898705 ACAGAGAAATCAGCGATCCAC 58.101 47.619 0.00 0.00 0.00 4.02
558 574 7.492524 TGAGTATTAACAGAGAAATCAGCGAT 58.507 34.615 0.00 0.00 0.00 4.58
561 577 8.485976 AACTGAGTATTAACAGAGAAATCAGC 57.514 34.615 0.00 0.00 36.06 4.26
576 592 9.236006 AGCATCATAGAACAAAAACTGAGTATT 57.764 29.630 0.00 0.00 0.00 1.89
579 595 7.661437 TGTAGCATCATAGAACAAAAACTGAGT 59.339 33.333 0.00 0.00 0.00 3.41
588 604 9.489084 GGTGTATTATGTAGCATCATAGAACAA 57.511 33.333 13.53 0.60 33.23 2.83
656 681 7.824289 TCAAACATTGAGAAGTTATAGACCTGG 59.176 37.037 0.00 0.00 34.08 4.45
659 684 9.383519 TGATCAAACATTGAGAAGTTATAGACC 57.616 33.333 0.00 0.00 43.98 3.85
666 691 9.657419 AAAAACTTGATCAAACATTGAGAAGTT 57.343 25.926 18.22 18.22 46.95 2.66
688 713 9.651913 AGAGTTTGCTGTTTTTCTCAATAAAAA 57.348 25.926 0.00 0.00 36.30 1.94
695 720 5.189928 TGGTAGAGTTTGCTGTTTTTCTCA 58.810 37.500 0.00 0.00 0.00 3.27
704 729 7.144722 TGAATTTGTATGGTAGAGTTTGCTG 57.855 36.000 0.00 0.00 0.00 4.41
847 907 0.832983 AGTAACTGGCCCCACGTGTA 60.833 55.000 15.65 0.00 0.00 2.90
851 911 0.974010 TAGGAGTAACTGGCCCCACG 60.974 60.000 0.00 0.00 0.00 4.94
866 926 4.521146 AGAGAGAAATAACCGTCGTAGGA 58.479 43.478 5.97 0.00 34.73 2.94
870 930 3.354467 AGGAGAGAGAAATAACCGTCGT 58.646 45.455 0.00 0.00 0.00 4.34
878 938 6.095160 GTCCACGTAGAAAGGAGAGAGAAATA 59.905 42.308 0.00 0.00 30.78 1.40
954 1027 4.150454 AGCCGAGGGGAGGAGAGG 62.150 72.222 0.00 0.00 34.06 3.69
1218 1303 4.421554 CAGGAGAGGGGCAGGGGA 62.422 72.222 0.00 0.00 0.00 4.81
1219 1304 4.748798 ACAGGAGAGGGGCAGGGG 62.749 72.222 0.00 0.00 0.00 4.79
1220 1305 2.612115 AACAGGAGAGGGGCAGGG 60.612 66.667 0.00 0.00 0.00 4.45
1224 1309 3.412408 GGGGAACAGGAGAGGGGC 61.412 72.222 0.00 0.00 0.00 5.80
1320 1411 7.093354 GGCATATTGAGAGATTAATCGACAGA 58.907 38.462 9.78 4.88 0.00 3.41
1330 1421 5.597182 AGCACAATTGGCATATTGAGAGATT 59.403 36.000 21.19 0.59 38.56 2.40
1331 1422 5.138276 AGCACAATTGGCATATTGAGAGAT 58.862 37.500 21.19 11.23 38.56 2.75
1342 1448 2.628696 CCGCTGAGCACAATTGGCA 61.629 57.895 17.54 6.93 0.00 4.92
1424 1530 3.248602 CACTGGTAAGCTCATTATTCGGC 59.751 47.826 0.00 0.00 0.00 5.54
1431 1537 4.207165 ACACAAACACTGGTAAGCTCATT 58.793 39.130 0.00 0.00 0.00 2.57
1441 1547 1.677576 ACATGCAGACACAAACACTGG 59.322 47.619 0.00 0.00 33.00 4.00
1442 1548 3.110358 CAACATGCAGACACAAACACTG 58.890 45.455 0.00 0.00 35.14 3.66
1467 1573 0.523072 CCGTGAATGCAGAACCCAAG 59.477 55.000 0.00 0.00 0.00 3.61
1488 1594 3.244735 TGGGCAGCAGTTTACATACTCAA 60.245 43.478 0.00 0.00 0.00 3.02
1689 1915 6.371548 TCCTAAACTGAACATCATGTTAGCAC 59.628 38.462 2.04 0.00 41.28 4.40
1787 2013 4.306600 GGACCAACAAAATGTCCAATGTC 58.693 43.478 3.14 0.00 46.29 3.06
1830 2066 2.280628 GTAGGGCGATCTGAAAAGTGG 58.719 52.381 0.00 0.00 0.00 4.00
1850 2086 0.613260 TGTTCCATCGACCTTCCAGG 59.387 55.000 0.00 0.00 42.49 4.45
1899 2135 4.339872 ACAAAAGCTTGGATGCAAATGA 57.660 36.364 0.00 0.00 36.82 2.57
1928 2164 2.804986 TGCATCCAGAAATAGTGGCA 57.195 45.000 0.00 0.00 34.77 4.92
1979 2215 3.008485 AGAACAAAGTAAGGGGAGCTCTG 59.992 47.826 14.64 2.87 0.00 3.35
1987 2223 5.799213 ACTCTCATGAGAACAAAGTAAGGG 58.201 41.667 25.09 11.85 42.73 3.95
1997 2233 5.462405 ACGTAACTCAACTCTCATGAGAAC 58.538 41.667 25.09 16.31 45.74 3.01
2039 2275 6.513806 TGTATCTGCAACACAGCATTTAAT 57.486 33.333 0.00 0.00 46.76 1.40
2042 2278 5.415389 TGTATGTATCTGCAACACAGCATTT 59.585 36.000 0.00 0.00 46.76 2.32
2043 2279 4.943093 TGTATGTATCTGCAACACAGCATT 59.057 37.500 0.00 0.00 46.76 3.56
2075 2311 9.513906 TGATACACATTTTGTCAAAGGAAGATA 57.486 29.630 0.00 0.00 39.91 1.98
2081 2317 9.669353 GCTATATGATACACATTTTGTCAAAGG 57.331 33.333 0.00 0.00 39.91 3.11
2108 2345 4.042187 ACCTCCTGTGAAAAGAGCATACTT 59.958 41.667 0.00 0.00 0.00 2.24
2123 2360 1.971357 CACTTGTAGGTGACCTCCTGT 59.029 52.381 7.77 0.09 39.34 4.00
2124 2361 1.971357 ACACTTGTAGGTGACCTCCTG 59.029 52.381 7.77 0.00 40.13 3.86
2202 2439 4.992951 ACCGTATTAAAGAGCTTGACGTTT 59.007 37.500 0.00 0.00 0.00 3.60
2217 2454 9.491675 TTCACAACTTCTGAAATTACCGTATTA 57.508 29.630 0.00 0.00 0.00 0.98
2233 2470 6.716438 GTTGTAGGAGACTTTTCACAACTTC 58.284 40.000 7.86 0.00 45.89 3.01
2249 2486 4.705337 AAAACGCACAAAAGTTGTAGGA 57.295 36.364 0.00 0.00 43.23 2.94
2258 2495 4.339814 AGATAGACCCAAAAACGCACAAAA 59.660 37.500 0.00 0.00 0.00 2.44
2259 2496 3.886505 AGATAGACCCAAAAACGCACAAA 59.113 39.130 0.00 0.00 0.00 2.83
2274 2511 6.109359 ACATGAGGTAGTTGCAAAGATAGAC 58.891 40.000 0.00 0.00 0.00 2.59
2284 2521 4.218417 ACATTGGAAACATGAGGTAGTTGC 59.782 41.667 0.00 0.00 42.32 4.17
2321 2558 0.830648 TGCATGCTGTAGGGAGGTAC 59.169 55.000 20.33 0.00 0.00 3.34
2327 2564 2.916702 TAGATGTGCATGCTGTAGGG 57.083 50.000 20.33 0.00 0.00 3.53
2358 2595 7.995289 AGACACACACTGTAATTTCATTTTGA 58.005 30.769 0.00 0.00 31.03 2.69
2359 2596 8.633075 AAGACACACACTGTAATTTCATTTTG 57.367 30.769 0.00 0.00 31.03 2.44
2362 2599 6.772716 AGGAAGACACACACTGTAATTTCATT 59.227 34.615 0.00 0.00 31.03 2.57
2363 2600 6.299141 AGGAAGACACACACTGTAATTTCAT 58.701 36.000 0.00 0.00 31.03 2.57
2364 2601 5.680619 AGGAAGACACACACTGTAATTTCA 58.319 37.500 0.00 0.00 31.03 2.69
2365 2602 6.619801 AAGGAAGACACACACTGTAATTTC 57.380 37.500 0.00 0.00 31.03 2.17
2367 2604 7.936847 TCATAAAGGAAGACACACACTGTAATT 59.063 33.333 0.00 0.00 31.03 1.40
2368 2605 7.387948 GTCATAAAGGAAGACACACACTGTAAT 59.612 37.037 0.00 0.00 31.03 1.89
2369 2606 6.704493 GTCATAAAGGAAGACACACACTGTAA 59.296 38.462 0.00 0.00 31.03 2.41
2370 2607 6.220930 GTCATAAAGGAAGACACACACTGTA 58.779 40.000 0.00 0.00 31.03 2.74
2371 2608 5.057149 GTCATAAAGGAAGACACACACTGT 58.943 41.667 0.00 0.00 34.96 3.55
2372 2609 4.452455 GGTCATAAAGGAAGACACACACTG 59.548 45.833 0.00 0.00 34.04 3.66
2373 2610 4.348168 AGGTCATAAAGGAAGACACACACT 59.652 41.667 0.00 0.00 34.04 3.55
2374 2611 4.452455 CAGGTCATAAAGGAAGACACACAC 59.548 45.833 0.00 0.00 34.04 3.82
2375 2612 4.102524 ACAGGTCATAAAGGAAGACACACA 59.897 41.667 0.00 0.00 34.04 3.72
2376 2613 4.642429 ACAGGTCATAAAGGAAGACACAC 58.358 43.478 0.00 0.00 34.04 3.82
2377 2614 4.974645 ACAGGTCATAAAGGAAGACACA 57.025 40.909 0.00 0.00 34.04 3.72
2378 2615 4.870991 GCTACAGGTCATAAAGGAAGACAC 59.129 45.833 0.00 0.00 34.04 3.67
2379 2616 4.777896 AGCTACAGGTCATAAAGGAAGACA 59.222 41.667 0.00 0.00 34.04 3.41
2380 2617 5.128008 AGAGCTACAGGTCATAAAGGAAGAC 59.872 44.000 10.78 0.00 44.42 3.01
2381 2618 5.273208 AGAGCTACAGGTCATAAAGGAAGA 58.727 41.667 10.78 0.00 44.42 2.87
2382 2619 5.606348 AGAGCTACAGGTCATAAAGGAAG 57.394 43.478 10.78 0.00 44.42 3.46
2383 2620 5.248477 ACAAGAGCTACAGGTCATAAAGGAA 59.752 40.000 10.78 0.00 44.42 3.36
2384 2621 4.777896 ACAAGAGCTACAGGTCATAAAGGA 59.222 41.667 10.78 0.00 44.42 3.36
2385 2622 5.091261 ACAAGAGCTACAGGTCATAAAGG 57.909 43.478 10.78 0.00 44.42 3.11
2386 2623 8.200792 AGATTACAAGAGCTACAGGTCATAAAG 58.799 37.037 10.78 0.00 44.42 1.85
2387 2624 7.981789 CAGATTACAAGAGCTACAGGTCATAAA 59.018 37.037 10.78 0.91 44.42 1.40
2394 2631 5.330455 TGTCAGATTACAAGAGCTACAGG 57.670 43.478 0.00 0.00 0.00 4.00
2411 2648 5.738909 AGTATGAACTTGGGATCTTGTCAG 58.261 41.667 0.00 0.00 29.00 3.51
2414 2651 6.653989 CCTTAGTATGAACTTGGGATCTTGT 58.346 40.000 0.00 0.00 37.15 3.16
2421 2658 6.260936 CAGTAATGCCTTAGTATGAACTTGGG 59.739 42.308 0.00 0.00 37.15 4.12
2443 2688 2.240667 AGACAGATAAATGGCTGCCAGT 59.759 45.455 27.20 22.45 37.09 4.00
2472 2717 0.032813 AATTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2474 2719 0.388294 GTAATTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2475 2720 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.000 13.64 0.00 46.06 4.20
2476 2721 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2477 2722 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2478 2723 2.537401 GACAAGTAATTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2479 2724 1.135315 CGACAAGTAATTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2481 2726 0.643820 GCGACAAGTAATTCCGGACG 59.356 55.000 1.83 1.53 0.00 4.79
2482 2727 1.004595 GGCGACAAGTAATTCCGGAC 58.995 55.000 1.83 0.00 0.00 4.79
2483 2728 0.458889 CGGCGACAAGTAATTCCGGA 60.459 55.000 0.00 0.00 33.85 5.14
2484 2729 0.458889 TCGGCGACAAGTAATTCCGG 60.459 55.000 4.99 0.00 37.65 5.14
2485 2730 1.352114 TTCGGCGACAAGTAATTCCG 58.648 50.000 10.16 0.00 38.34 4.30
2486 2731 3.372822 TCATTTCGGCGACAAGTAATTCC 59.627 43.478 10.16 0.00 0.00 3.01
2487 2732 4.593597 TCATTTCGGCGACAAGTAATTC 57.406 40.909 10.16 0.00 0.00 2.17
2488 2733 5.560966 ATTCATTTCGGCGACAAGTAATT 57.439 34.783 10.16 0.00 0.00 1.40
2489 2734 6.671614 TTATTCATTTCGGCGACAAGTAAT 57.328 33.333 10.16 3.05 0.00 1.89
2490 2735 6.483385 TTTATTCATTTCGGCGACAAGTAA 57.517 33.333 10.16 0.01 0.00 2.24
2491 2736 6.483385 TTTTATTCATTTCGGCGACAAGTA 57.517 33.333 10.16 0.00 0.00 2.24
2492 2737 5.365403 TTTTATTCATTTCGGCGACAAGT 57.635 34.783 10.16 0.00 0.00 3.16
2493 2738 6.237542 CCATTTTTATTCATTTCGGCGACAAG 60.238 38.462 10.16 0.00 0.00 3.16
2494 2739 5.574830 CCATTTTTATTCATTTCGGCGACAA 59.425 36.000 10.16 8.07 0.00 3.18
2495 2740 5.098893 CCATTTTTATTCATTTCGGCGACA 58.901 37.500 10.16 2.52 0.00 4.35
2496 2741 5.336744 TCCATTTTTATTCATTTCGGCGAC 58.663 37.500 10.16 0.00 0.00 5.19
2497 2742 5.568685 TCCATTTTTATTCATTTCGGCGA 57.431 34.783 4.99 4.99 0.00 5.54
2498 2743 5.748152 ACATCCATTTTTATTCATTTCGGCG 59.252 36.000 0.00 0.00 0.00 6.46
2499 2744 8.816640 ATACATCCATTTTTATTCATTTCGGC 57.183 30.769 0.00 0.00 0.00 5.54
2528 2773 9.733556 TGGATGTATGTAGACATGTTTTACTTT 57.266 29.630 17.24 10.46 40.18 2.66
2529 2774 9.905713 ATGGATGTATGTAGACATGTTTTACTT 57.094 29.630 17.24 14.42 40.18 2.24
2530 2775 9.905713 AATGGATGTATGTAGACATGTTTTACT 57.094 29.630 17.24 6.54 40.18 2.24
2533 2778 9.241919 TGAAATGGATGTATGTAGACATGTTTT 57.758 29.630 0.00 0.00 40.18 2.43
2534 2779 8.806429 TGAAATGGATGTATGTAGACATGTTT 57.194 30.769 0.00 0.00 40.18 2.83
2535 2780 8.985315 ATGAAATGGATGTATGTAGACATGTT 57.015 30.769 0.00 0.00 40.18 2.71
2536 2781 8.843262 CAATGAAATGGATGTATGTAGACATGT 58.157 33.333 0.00 0.00 40.18 3.21
2537 2782 9.059260 TCAATGAAATGGATGTATGTAGACATG 57.941 33.333 5.39 0.00 40.18 3.21
2538 2783 9.060347 GTCAATGAAATGGATGTATGTAGACAT 57.940 33.333 0.08 0.08 42.82 3.06
2539 2784 8.046107 TGTCAATGAAATGGATGTATGTAGACA 58.954 33.333 0.00 0.00 0.00 3.41
2540 2785 8.437360 TGTCAATGAAATGGATGTATGTAGAC 57.563 34.615 0.00 0.00 0.00 2.59
2541 2786 9.112725 CTTGTCAATGAAATGGATGTATGTAGA 57.887 33.333 0.00 0.00 0.00 2.59
2542 2787 8.896744 ACTTGTCAATGAAATGGATGTATGTAG 58.103 33.333 0.00 0.00 0.00 2.74
2543 2788 8.806429 ACTTGTCAATGAAATGGATGTATGTA 57.194 30.769 0.00 0.00 0.00 2.29
2544 2789 7.707624 ACTTGTCAATGAAATGGATGTATGT 57.292 32.000 0.00 0.00 0.00 2.29
2548 2793 8.253113 GGAAATACTTGTCAATGAAATGGATGT 58.747 33.333 0.00 0.00 0.00 3.06
2549 2794 7.433131 CGGAAATACTTGTCAATGAAATGGATG 59.567 37.037 0.00 0.00 0.00 3.51
2550 2795 7.416664 CCGGAAATACTTGTCAATGAAATGGAT 60.417 37.037 0.00 0.00 0.00 3.41
2551 2796 6.127758 CCGGAAATACTTGTCAATGAAATGGA 60.128 38.462 0.00 0.00 0.00 3.41
2552 2797 6.035843 CCGGAAATACTTGTCAATGAAATGG 58.964 40.000 0.00 0.00 0.00 3.16
2553 2798 6.747280 GTCCGGAAATACTTGTCAATGAAATG 59.253 38.462 5.23 0.00 0.00 2.32
2554 2799 6.403200 CGTCCGGAAATACTTGTCAATGAAAT 60.403 38.462 5.23 0.00 0.00 2.17
2555 2800 5.106869 CGTCCGGAAATACTTGTCAATGAAA 60.107 40.000 5.23 0.00 0.00 2.69
2556 2801 4.390603 CGTCCGGAAATACTTGTCAATGAA 59.609 41.667 5.23 0.00 0.00 2.57
2557 2802 3.930229 CGTCCGGAAATACTTGTCAATGA 59.070 43.478 5.23 0.00 0.00 2.57
2558 2803 3.063452 CCGTCCGGAAATACTTGTCAATG 59.937 47.826 5.23 0.00 37.50 2.82
2559 2804 3.055675 TCCGTCCGGAAATACTTGTCAAT 60.056 43.478 5.23 0.00 42.05 2.57
2560 2805 2.299582 TCCGTCCGGAAATACTTGTCAA 59.700 45.455 5.23 0.00 42.05 3.18
2561 2806 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2562 2807 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2563 2808 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2564 2809 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2565 2810 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2566 2811 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2567 2812 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2568 2813 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2569 2814 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2570 2815 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
2571 2816 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
2572 2817 2.593978 CTACTCCCTCCGTCCGGA 59.406 66.667 0.00 0.00 42.90 5.14
2573 2818 2.335092 TAGCTACTCCCTCCGTCCGG 62.335 65.000 0.00 0.00 0.00 5.14
2574 2819 0.250814 ATAGCTACTCCCTCCGTCCG 60.251 60.000 0.00 0.00 0.00 4.79
2575 2820 2.875094 TATAGCTACTCCCTCCGTCC 57.125 55.000 0.00 0.00 0.00 4.79
2576 2821 6.377712 ACAAATATATAGCTACTCCCTCCGTC 59.622 42.308 0.00 0.00 0.00 4.79
2577 2822 6.254522 ACAAATATATAGCTACTCCCTCCGT 58.745 40.000 0.00 0.00 0.00 4.69
2578 2823 6.777213 ACAAATATATAGCTACTCCCTCCG 57.223 41.667 0.00 0.00 0.00 4.63
2631 2876 1.897560 AAGCAGTAAACTGTGAGGCC 58.102 50.000 11.54 0.00 45.45 5.19
2655 2904 8.301730 CAAATCTGTTTTGTATCTGCAAACAT 57.698 30.769 0.00 0.00 39.93 2.71
2688 2937 1.550327 CCTCCACAGACAGCTGAGTA 58.450 55.000 23.35 1.20 45.17 2.59
2694 2943 4.416738 GGCCCCTCCACAGACAGC 62.417 72.222 0.00 0.00 34.01 4.40
2700 2949 1.384502 CCTGATAGGCCCCTCCACA 60.385 63.158 0.00 0.00 37.29 4.17
2724 2973 1.777941 ATCCCTCAACGTACTCCTCC 58.222 55.000 0.00 0.00 0.00 4.30
2730 2979 5.217393 GTTTCCAAAAATCCCTCAACGTAC 58.783 41.667 0.00 0.00 0.00 3.67
2778 3027 0.538287 AGCCCTTCAGTTGTTCAGGC 60.538 55.000 0.00 0.00 39.25 4.85
2800 3049 1.187567 GCCCCTGCAGTTTGTCCAAT 61.188 55.000 13.81 0.00 37.47 3.16
2817 3066 1.807142 GCAGGAAGTTGTTGTAGAGCC 59.193 52.381 0.00 0.00 0.00 4.70
2826 3075 3.456277 CCCTTATAGAGGCAGGAAGTTGT 59.544 47.826 0.00 0.00 44.85 3.32
2847 3096 1.452108 CCCCTCCGAAACAGCATCC 60.452 63.158 0.00 0.00 0.00 3.51
2955 3206 4.285292 CTGCAGTTGTGTTGTCTGAATTC 58.715 43.478 5.25 0.00 0.00 2.17
2962 3213 3.715628 AAATCCTGCAGTTGTGTTGTC 57.284 42.857 13.81 0.00 0.00 3.18
2968 3219 5.648092 GGTCAGTAATAAATCCTGCAGTTGT 59.352 40.000 13.81 0.00 0.00 3.32
2973 3224 6.721318 AGAAAGGTCAGTAATAAATCCTGCA 58.279 36.000 0.00 0.00 0.00 4.41
2996 3247 5.460091 GCAAGCAGGAGTTTCTTTTAACAAG 59.540 40.000 0.00 0.00 0.00 3.16
2997 3248 5.127031 AGCAAGCAGGAGTTTCTTTTAACAA 59.873 36.000 0.00 0.00 0.00 2.83
2999 3250 5.188327 AGCAAGCAGGAGTTTCTTTTAAC 57.812 39.130 0.00 0.00 0.00 2.01
3000 3251 5.359576 TGAAGCAAGCAGGAGTTTCTTTTAA 59.640 36.000 0.00 0.00 0.00 1.52
3002 3253 3.701040 TGAAGCAAGCAGGAGTTTCTTTT 59.299 39.130 0.00 0.00 0.00 2.27
3006 3257 3.572584 CATTGAAGCAAGCAGGAGTTTC 58.427 45.455 0.00 0.00 0.00 2.78
3294 3546 9.561069 GGAACTAATCAATCCATGTAACATACT 57.439 33.333 0.00 0.00 33.30 2.12
3295 3547 8.495949 CGGAACTAATCAATCCATGTAACATAC 58.504 37.037 0.00 0.00 32.58 2.39
3619 3931 9.257651 GTATAGTCCAGTAATTATGTCCAACAC 57.742 37.037 0.00 0.00 0.00 3.32
3728 4040 3.250762 TGTGCAGCATTCAAACTCAGTAC 59.749 43.478 0.00 0.00 0.00 2.73
4002 4314 7.891183 TTTGTCTAAAAGAGAGGATCGAAAG 57.109 36.000 0.00 0.00 42.67 2.62
4003 4315 8.094548 TGATTTGTCTAAAAGAGAGGATCGAAA 58.905 33.333 0.00 0.00 42.67 3.46
4051 4363 5.514204 CGAGATTTCAAACCATTCATTCTGC 59.486 40.000 0.00 0.00 0.00 4.26
4159 4472 0.106335 CTCCAGCAGCATCTCGGATT 59.894 55.000 0.00 0.00 0.00 3.01
4219 4532 2.046285 GGGCGTGTTCTCCATTGGG 61.046 63.158 2.09 0.00 0.00 4.12
4237 4550 5.709966 TGATATTCCGGAATCACTACATCG 58.290 41.667 32.43 0.00 32.50 3.84
4252 4565 5.450550 GCCCAAACACTAGCTTTGATATTCC 60.451 44.000 12.89 0.00 31.32 3.01
4290 4603 7.881232 AGACATCTCCGAAAAAGTTAACCATAA 59.119 33.333 0.88 0.00 0.00 1.90
4355 4668 6.535150 TGACTGCTAACATATGCACTACTTTC 59.465 38.462 1.58 0.00 35.20 2.62
4436 4749 4.038042 CGAGTATTGCTCAACTCCAGGATA 59.962 45.833 2.63 0.00 44.33 2.59
4437 4750 3.181471 CGAGTATTGCTCAACTCCAGGAT 60.181 47.826 2.63 0.00 44.33 3.24
4458 4771 0.248784 TCATCGCATCTGACTGCTCG 60.249 55.000 9.33 0.00 40.06 5.03
4464 4777 5.680229 CAGCTAATTTTTCATCGCATCTGAC 59.320 40.000 0.00 0.00 0.00 3.51
4486 4799 1.164411 TTACTGCCCATTTCGCACAG 58.836 50.000 0.00 0.00 31.61 3.66
4488 4801 2.939460 ATTTACTGCCCATTTCGCAC 57.061 45.000 0.00 0.00 31.61 5.34
4601 8820 6.441093 TGCTGGATGTTTGTATTTGAGATC 57.559 37.500 0.00 0.00 0.00 2.75
4628 8847 3.316308 GCCACATGATCCACATTTCTACC 59.684 47.826 0.00 0.00 37.07 3.18
4630 8849 3.053768 TGGCCACATGATCCACATTTCTA 60.054 43.478 0.00 0.00 37.07 2.10
4631 8850 2.291735 TGGCCACATGATCCACATTTCT 60.292 45.455 0.00 0.00 37.07 2.52
4684 8919 5.016831 GGGGAAGATTTTAGACACAATGGT 58.983 41.667 0.00 0.00 0.00 3.55
4692 8927 5.321927 TCCAACAAGGGGAAGATTTTAGAC 58.678 41.667 0.00 0.00 38.24 2.59
4713 8951 2.604046 ACGTACTCCTGATGCAATCC 57.396 50.000 0.00 0.00 44.73 3.01
4715 8953 7.441836 TGATTATTACGTACTCCTGATGCAAT 58.558 34.615 0.00 0.00 0.00 3.56
4716 8954 6.811954 TGATTATTACGTACTCCTGATGCAA 58.188 36.000 0.00 0.00 0.00 4.08
4718 8956 8.244802 ACTATGATTATTACGTACTCCTGATGC 58.755 37.037 0.00 0.00 0.00 3.91
4727 8965 9.994432 ACGGCTTATACTATGATTATTACGTAC 57.006 33.333 0.00 0.00 0.00 3.67
4729 8967 8.733458 TGACGGCTTATACTATGATTATTACGT 58.267 33.333 0.00 0.00 0.00 3.57
4730 8968 9.731819 ATGACGGCTTATACTATGATTATTACG 57.268 33.333 0.00 0.00 0.00 3.18
4763 9001 2.089980 GTTCAGGTAGAGTGCCGTCTA 58.910 52.381 0.00 0.00 0.00 2.59
4766 9004 0.603569 CAGTTCAGGTAGAGTGCCGT 59.396 55.000 0.00 0.00 0.00 5.68
4772 9018 8.091449 ACTAAACATTCTTCAGTTCAGGTAGAG 58.909 37.037 0.00 0.00 0.00 2.43
4988 9261 2.697751 CTGGGTGAACTAGAGGGAGATG 59.302 54.545 0.00 0.00 0.00 2.90
5023 9298 2.392662 TCCAACCTTCATTGTTTGCCA 58.607 42.857 0.00 0.00 0.00 4.92
5065 9340 4.846779 TGGCAGATTAGTTTGGTTGTTC 57.153 40.909 0.00 0.00 0.00 3.18
5118 9398 9.567776 TTCTCCAGTTTGTTGATATTTCAGTTA 57.432 29.630 0.00 0.00 32.27 2.24
5153 9434 3.644966 ATAGAATTGGGTTTCCTGCGA 57.355 42.857 0.00 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.