Multiple sequence alignment - TraesCS5A01G145700

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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 TraesCS5A01G145700 chr5A 100.000 7137 0 0 1 7137 321922783 321915647 0.000000e+00 13180.0
1 TraesCS5A01G145700 chr5A 96.610 59 2 0 2153 2211 321920587 321920529 1.640000e-16 99.0
2 TraesCS5A01G145700 chr5A 96.610 59 2 0 2197 2255 321920631 321920573 1.640000e-16 99.0
3 TraesCS5A01G145700 chr5A 96.875 32 1 0 2467 2498 321920148 321920117 4.000000e-03 54.7
4 TraesCS5A01G145700 chr5A 96.875 32 1 0 2636 2667 321920317 321920286 4.000000e-03 54.7
5 TraesCS5A01G145700 chr5D 93.113 2817 123 26 3526 6297 233046482 233049272 0.000000e+00 4061.0
6 TraesCS5A01G145700 chr5D 92.522 2514 83 32 1 2466 233042444 233044900 0.000000e+00 3504.0
7 TraesCS5A01G145700 chr5D 95.519 491 22 0 3029 3519 233045520 233046010 0.000000e+00 785.0
8 TraesCS5A01G145700 chr5D 88.744 613 50 12 6535 7137 233055317 233055920 0.000000e+00 732.0
9 TraesCS5A01G145700 chr5D 94.607 445 14 5 2594 3029 233044897 233045340 0.000000e+00 680.0
10 TraesCS5A01G145700 chr5D 90.446 157 9 3 6375 6525 233054267 233054423 1.210000e-47 202.0
11 TraesCS5A01G145700 chr5D 96.610 59 2 0 2197 2255 233044595 233044653 1.640000e-16 99.0
12 TraesCS5A01G145700 chr5D 89.394 66 0 1 2153 2211 233044639 233044704 7.680000e-10 76.8
13 TraesCS5A01G145700 chr5D 100.000 29 0 0 2467 2495 233044943 233044971 4.000000e-03 54.7
14 TraesCS5A01G145700 chr5B 93.848 2666 95 30 4504 7137 271941855 271939227 0.000000e+00 3951.0
15 TraesCS5A01G145700 chr5B 93.178 2023 90 16 1 1994 271946156 271944153 0.000000e+00 2928.0
16 TraesCS5A01G145700 chr5B 89.982 549 41 6 3031 3574 271943362 271942823 0.000000e+00 697.0
17 TraesCS5A01G145700 chr5B 90.959 365 25 4 2673 3029 271943878 271943514 1.080000e-132 484.0
18 TraesCS5A01G145700 chr5B 89.941 338 28 6 4168 4501 271942340 271942005 1.420000e-116 431.0
19 TraesCS5A01G145700 chr5B 92.157 102 5 2 2228 2326 271944147 271944046 2.680000e-29 141.0
20 TraesCS5A01G145700 chr5B 83.133 83 4 1 3571 3643 271942434 271942352 4.620000e-07 67.6
21 TraesCS5A01G145700 chr5B 100.000 28 0 0 2184 2211 271944147 271944120 1.300000e-02 52.8
22 TraesCS5A01G145700 chr2A 86.053 674 75 10 1 662 471038994 471038328 0.000000e+00 706.0
23 TraesCS5A01G145700 chr1D 94.304 158 6 2 2002 2157 7349856 7349700 9.250000e-59 239.0
24 TraesCS5A01G145700 chr3D 92.308 169 10 2 1993 2158 322435282 322435450 3.330000e-58 237.0
25 TraesCS5A01G145700 chr3B 92.308 169 10 2 1993 2158 396271869 396272037 3.330000e-58 237.0
26 TraesCS5A01G145700 chr3B 96.875 32 1 0 6222 6253 239245668 239245699 4.000000e-03 54.7
27 TraesCS5A01G145700 chr4D 93.168 161 8 2 1996 2153 74079344 74079504 4.300000e-57 233.0
28 TraesCS5A01G145700 chr4A 93.125 160 8 3 2003 2159 460230649 460230808 1.550000e-56 231.0
29 TraesCS5A01G145700 chr4A 92.453 159 11 1 1996 2153 514080170 514080012 7.200000e-55 226.0
30 TraesCS5A01G145700 chr2D 93.125 160 8 2 2002 2158 79056166 79056325 1.550000e-56 231.0
31 TraesCS5A01G145700 chr6B 86.700 203 21 3 474 670 205938018 205938220 3.350000e-53 220.0
32 TraesCS5A01G145700 chr6B 90.000 50 3 2 2328 2375 534091787 534091738 5.980000e-06 63.9
33 TraesCS5A01G145700 chr7D 87.895 190 15 8 1973 2156 447053688 447053501 4.340000e-52 217.0
34 TraesCS5A01G145700 chr7B 93.750 48 3 0 2329 2376 674078410 674078363 9.930000e-09 73.1


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 TraesCS5A01G145700 chr5A 321915647 321922783 7136 True 2697.480000 13180 97.394000 1 7137 5 chr5A.!!$R1 7136
1 TraesCS5A01G145700 chr5D 233042444 233049272 6828 False 1322.928571 4061 94.537857 1 6297 7 chr5D.!!$F1 6296
2 TraesCS5A01G145700 chr5D 233054267 233055920 1653 False 467.000000 732 89.595000 6375 7137 2 chr5D.!!$F2 762
3 TraesCS5A01G145700 chr5B 271939227 271946156 6929 True 1094.050000 3951 91.649750 1 7137 8 chr5B.!!$R1 7136
4 TraesCS5A01G145700 chr2A 471038328 471038994 666 True 706.000000 706 86.053000 1 662 1 chr2A.!!$R1 661

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
670 683 2.017049 GCCAGAACGTATTTGCCTGAT 58.983 47.619 0.00 0.00 0.00 2.90 F
1091 1110 1.183549 TGGCTAAGACCGGAGAAGAC 58.816 55.000 9.46 2.14 0.00 3.01 F
2013 2085 1.275573 GCAAAGAAGTACTCCCTCCGT 59.724 52.381 0.00 0.00 0.00 4.69 F
3300 3602 0.106149 GAACTGGTCGTTGAGGGTGT 59.894 55.000 0.00 0.00 35.56 4.16 F
4126 5303 0.250640 GCTGCCTGCATAGCCAGTAT 60.251 55.000 6.42 0.00 42.31 2.12 F
4194 5371 0.601311 GCGAAGTGTGCTGAGAAGGT 60.601 55.000 0.00 0.00 0.00 3.50 F
5335 6698 0.310854 GAACTGGCAAAGGACAACGG 59.689 55.000 0.00 0.00 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2418 2503 0.676782 GCAACTTAGCGGTGGTGGAT 60.677 55.0 0.00 0.0 0.00 3.41 R
2665 2754 2.096496 GTGCACACAGTCATGGCTTATC 59.904 50.0 13.17 0.0 0.00 1.75 R
3823 5000 0.037326 GTGATCCAACTGTCGCCTCA 60.037 55.0 0.00 0.0 0.00 3.86 R
4214 5391 0.830648 CGGCCTAAGAACCATCTGGA 59.169 55.0 0.00 0.0 35.59 3.86 R
5335 6698 0.172352 CTCAGCTCCACTCTCGTTCC 59.828 60.0 0.00 0.0 0.00 3.62 R
5344 6707 0.251354 TGCCTCATTCTCAGCTCCAC 59.749 55.0 0.00 0.0 0.00 4.02 R
6492 7865 0.249120 CAGGGTGAAGTATGCGGACA 59.751 55.0 0.00 0.0 0.00 4.02 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
79 80 4.038282 TGATCTTGTGTGAGCATGCTTTTT 59.962 37.500 23.61 0.00 0.00 1.94
414 415 8.072480 ACTGGATAGTCCTAACCTTATAGGTTT 58.928 37.037 15.65 1.33 46.15 3.27
648 661 3.690628 CACATGCCATCTGTTGTATGTCA 59.309 43.478 0.00 0.00 32.21 3.58
670 683 2.017049 GCCAGAACGTATTTGCCTGAT 58.983 47.619 0.00 0.00 0.00 2.90
721 735 4.887071 TGTTAAATCTGGTTGTCAGTTGCT 59.113 37.500 0.00 0.00 43.76 3.91
912 927 5.048852 TCAGATTCATATGCTCAGAGACTCG 60.049 44.000 0.00 0.00 0.00 4.18
918 933 2.713895 TGCTCAGAGACTCGAACAAG 57.286 50.000 0.00 0.00 0.00 3.16
991 1010 3.790437 CCGCCTCCAGCTCCATGT 61.790 66.667 0.00 0.00 40.39 3.21
1066 1085 3.857093 AGCTTTGTTTTGCTTGTGTAACG 59.143 39.130 0.00 0.00 35.86 3.18
1091 1110 1.183549 TGGCTAAGACCGGAGAAGAC 58.816 55.000 9.46 2.14 0.00 3.01
1116 1135 1.734655 AGAGGTTGAGAAGGCAAGGA 58.265 50.000 0.00 0.00 0.00 3.36
1279 1298 9.200817 AGGAAATTTATGGTATGTATGCAAGTT 57.799 29.630 0.00 0.00 0.00 2.66
1308 1327 7.812690 TTGATGCTATGATCTTGCTATGTTT 57.187 32.000 0.00 0.00 0.00 2.83
1486 1507 9.814899 TTTGATTGATTTGTACACTGACATTTT 57.185 25.926 0.00 0.00 0.00 1.82
1555 1583 2.325583 AACAGCGGTTGTCAGAGAAA 57.674 45.000 0.00 0.00 39.73 2.52
1562 1590 3.535561 CGGTTGTCAGAGAAATGGCTAT 58.464 45.455 0.00 0.00 0.00 2.97
1563 1591 3.310774 CGGTTGTCAGAGAAATGGCTATG 59.689 47.826 0.00 0.00 0.00 2.23
1771 1803 3.914426 ACTTCTGTTGTCAGTTGTCCT 57.086 42.857 0.00 0.00 41.91 3.85
1998 2070 6.413018 AAAGCTCAAAACAAGAAAGCAAAG 57.587 33.333 0.00 0.00 35.42 2.77
2013 2085 1.275573 GCAAAGAAGTACTCCCTCCGT 59.724 52.381 0.00 0.00 0.00 4.69
2024 2096 6.637657 AGTACTCCCTCCGTTTACAAATAAG 58.362 40.000 0.00 0.00 0.00 1.73
2095 2167 5.647658 TGTGTTTGTTCACTCATTTCAGTCT 59.352 36.000 0.00 0.00 38.90 3.24
2278 2363 6.313324 AGTAGAACTACAGTCTACAACCCTT 58.687 40.000 13.34 0.00 38.90 3.95
2339 2424 8.427276 AGGTTAGTACATACTATTAAACTGCCC 58.573 37.037 0.00 0.00 38.48 5.36
2340 2425 8.427276 GGTTAGTACATACTATTAAACTGCCCT 58.573 37.037 0.00 0.00 38.48 5.19
2341 2426 9.257651 GTTAGTACATACTATTAAACTGCCCTG 57.742 37.037 0.00 0.00 38.48 4.45
2342 2427 7.670605 AGTACATACTATTAAACTGCCCTGA 57.329 36.000 0.00 0.00 34.13 3.86
2343 2428 7.498443 AGTACATACTATTAAACTGCCCTGAC 58.502 38.462 0.00 0.00 34.13 3.51
2344 2429 5.357257 ACATACTATTAAACTGCCCTGACG 58.643 41.667 0.00 0.00 0.00 4.35
2345 2430 3.975168 ACTATTAAACTGCCCTGACGT 57.025 42.857 0.00 0.00 0.00 4.34
2346 2431 3.858247 ACTATTAAACTGCCCTGACGTC 58.142 45.455 9.11 9.11 0.00 4.34
2347 2432 3.514309 ACTATTAAACTGCCCTGACGTCT 59.486 43.478 17.92 0.00 0.00 4.18
2348 2433 2.922740 TTAAACTGCCCTGACGTCTT 57.077 45.000 17.92 2.32 0.00 3.01
2349 2434 4.546829 ATTAAACTGCCCTGACGTCTTA 57.453 40.909 17.92 1.29 0.00 2.10
2350 2435 4.546829 TTAAACTGCCCTGACGTCTTAT 57.453 40.909 17.92 0.00 0.00 1.73
2351 2436 5.664294 TTAAACTGCCCTGACGTCTTATA 57.336 39.130 17.92 0.00 0.00 0.98
2352 2437 4.755266 AAACTGCCCTGACGTCTTATAT 57.245 40.909 17.92 0.00 0.00 0.86
2353 2438 3.735237 ACTGCCCTGACGTCTTATATG 57.265 47.619 17.92 5.92 0.00 1.78
2354 2439 3.031736 ACTGCCCTGACGTCTTATATGT 58.968 45.455 17.92 6.54 0.00 2.29
2355 2440 4.212716 ACTGCCCTGACGTCTTATATGTA 58.787 43.478 17.92 0.00 0.00 2.29
2356 2441 4.278669 ACTGCCCTGACGTCTTATATGTAG 59.721 45.833 17.92 10.11 0.00 2.74
2357 2442 3.572682 TGCCCTGACGTCTTATATGTAGG 59.427 47.826 17.92 11.87 0.00 3.18
2418 2503 7.238486 ACCAAATACTTTTATGGACAATGCA 57.762 32.000 0.00 0.00 36.75 3.96
2428 2513 1.656818 GGACAATGCATCCACCACCG 61.657 60.000 0.00 0.00 36.15 4.94
2468 2554 8.421673 AGTGTGTTTAAACTTGAGAAGTACTC 57.578 34.615 18.72 6.73 41.91 2.59
2469 2555 7.494952 AGTGTGTTTAAACTTGAGAAGTACTCC 59.505 37.037 18.72 0.00 44.34 3.85
2470 2556 6.764560 TGTGTTTAAACTTGAGAAGTACTCCC 59.235 38.462 18.72 0.00 44.34 4.30
2472 2558 7.498239 GTGTTTAAACTTGAGAAGTACTCCCTT 59.502 37.037 18.72 0.00 44.34 3.95
2473 2559 7.497909 TGTTTAAACTTGAGAAGTACTCCCTTG 59.502 37.037 18.72 0.00 44.34 3.61
2474 2560 5.888982 AAACTTGAGAAGTACTCCCTTGA 57.111 39.130 0.00 0.00 44.34 3.02
2475 2561 4.875561 ACTTGAGAAGTACTCCCTTGAC 57.124 45.455 0.00 0.00 44.34 3.18
2476 2562 4.223953 ACTTGAGAAGTACTCCCTTGACA 58.776 43.478 0.00 0.00 44.34 3.58
2477 2563 4.654262 ACTTGAGAAGTACTCCCTTGACAA 59.346 41.667 0.00 0.00 44.34 3.18
2478 2564 4.873746 TGAGAAGTACTCCCTTGACAAG 57.126 45.455 8.31 8.31 44.34 3.16
2479 2565 4.223953 TGAGAAGTACTCCCTTGACAAGT 58.776 43.478 14.03 0.00 44.34 3.16
2480 2566 4.039245 TGAGAAGTACTCCCTTGACAAGTG 59.961 45.833 14.03 2.73 44.34 3.16
2481 2567 4.223953 AGAAGTACTCCCTTGACAAGTGA 58.776 43.478 14.03 7.30 0.00 3.41
2482 2568 4.654262 AGAAGTACTCCCTTGACAAGTGAA 59.346 41.667 14.03 0.00 0.00 3.18
2483 2569 5.308237 AGAAGTACTCCCTTGACAAGTGAAT 59.692 40.000 14.03 0.57 0.00 2.57
2484 2570 5.568620 AGTACTCCCTTGACAAGTGAATT 57.431 39.130 14.03 1.31 0.00 2.17
2485 2571 5.941788 AGTACTCCCTTGACAAGTGAATTT 58.058 37.500 14.03 0.00 0.00 1.82
2486 2572 5.765182 AGTACTCCCTTGACAAGTGAATTTG 59.235 40.000 14.03 0.00 0.00 2.32
2487 2573 4.536765 ACTCCCTTGACAAGTGAATTTGT 58.463 39.130 14.03 0.08 43.61 2.83
2488 2574 4.956075 ACTCCCTTGACAAGTGAATTTGTT 59.044 37.500 14.03 0.00 41.15 2.83
2489 2575 5.422012 ACTCCCTTGACAAGTGAATTTGTTT 59.578 36.000 14.03 0.00 41.15 2.83
2490 2576 6.070824 ACTCCCTTGACAAGTGAATTTGTTTT 60.071 34.615 14.03 0.00 41.15 2.43
2491 2577 6.706295 TCCCTTGACAAGTGAATTTGTTTTT 58.294 32.000 14.03 0.00 41.15 1.94
2492 2578 6.593382 TCCCTTGACAAGTGAATTTGTTTTTG 59.407 34.615 14.03 0.00 41.15 2.44
2493 2579 6.250089 CCTTGACAAGTGAATTTGTTTTTGC 58.750 36.000 14.03 0.00 41.15 3.68
2494 2580 6.128336 CCTTGACAAGTGAATTTGTTTTTGCA 60.128 34.615 14.03 0.00 41.15 4.08
2495 2581 6.791887 TGACAAGTGAATTTGTTTTTGCAA 57.208 29.167 0.00 0.00 41.15 4.08
2496 2582 6.829703 TGACAAGTGAATTTGTTTTTGCAAG 58.170 32.000 0.00 0.00 41.15 4.01
2497 2583 6.648310 TGACAAGTGAATTTGTTTTTGCAAGA 59.352 30.769 0.00 0.00 41.15 3.02
2498 2584 7.172190 TGACAAGTGAATTTGTTTTTGCAAGAA 59.828 29.630 0.00 0.00 41.15 2.52
2499 2585 7.520686 ACAAGTGAATTTGTTTTTGCAAGAAG 58.479 30.769 2.07 0.00 38.05 2.85
2500 2586 7.173047 ACAAGTGAATTTGTTTTTGCAAGAAGT 59.827 29.630 2.07 0.00 38.05 3.01
2501 2587 8.655092 CAAGTGAATTTGTTTTTGCAAGAAGTA 58.345 29.630 2.07 0.00 0.00 2.24
2502 2588 8.947055 AGTGAATTTGTTTTTGCAAGAAGTAT 57.053 26.923 2.07 0.00 0.00 2.12
2503 2589 9.382275 AGTGAATTTGTTTTTGCAAGAAGTATT 57.618 25.926 2.07 3.61 0.00 1.89
2515 2601 9.912634 TTTGCAAGAAGTATTAGATTTTCCTTG 57.087 29.630 0.00 0.00 0.00 3.61
2516 2602 8.862325 TGCAAGAAGTATTAGATTTTCCTTGA 57.138 30.769 0.00 0.00 0.00 3.02
2517 2603 8.730680 TGCAAGAAGTATTAGATTTTCCTTGAC 58.269 33.333 0.00 0.00 0.00 3.18
2518 2604 8.730680 GCAAGAAGTATTAGATTTTCCTTGACA 58.269 33.333 0.00 0.00 0.00 3.58
2523 2609 9.793259 AAGTATTAGATTTTCCTTGACAAGTGA 57.207 29.630 14.03 8.12 0.00 3.41
2524 2610 9.793259 AGTATTAGATTTTCCTTGACAAGTGAA 57.207 29.630 14.03 13.09 0.00 3.18
2528 2614 9.748708 TTAGATTTTCCTTGACAAGTGAATTTG 57.251 29.630 14.03 0.00 0.00 2.32
2529 2615 7.785033 AGATTTTCCTTGACAAGTGAATTTGT 58.215 30.769 14.03 4.51 43.61 2.83
2530 2616 8.260114 AGATTTTCCTTGACAAGTGAATTTGTT 58.740 29.630 14.03 2.31 41.15 2.83
2531 2617 8.791327 ATTTTCCTTGACAAGTGAATTTGTTT 57.209 26.923 14.03 0.00 41.15 2.83
2532 2618 9.883142 ATTTTCCTTGACAAGTGAATTTGTTTA 57.117 25.926 14.03 0.00 41.15 2.01
2533 2619 9.712305 TTTTCCTTGACAAGTGAATTTGTTTAA 57.288 25.926 14.03 4.59 41.15 1.52
2534 2620 9.712305 TTTCCTTGACAAGTGAATTTGTTTAAA 57.288 25.926 14.03 0.00 41.15 1.52
2535 2621 8.925161 TCCTTGACAAGTGAATTTGTTTAAAG 57.075 30.769 14.03 0.00 41.15 1.85
2536 2622 7.978975 TCCTTGACAAGTGAATTTGTTTAAAGG 59.021 33.333 14.03 15.24 41.15 3.11
2537 2623 7.978975 CCTTGACAAGTGAATTTGTTTAAAGGA 59.021 33.333 14.03 0.00 42.11 3.36
2538 2624 9.533253 CTTGACAAGTGAATTTGTTTAAAGGAT 57.467 29.630 7.05 0.00 41.15 3.24
2539 2625 8.870160 TGACAAGTGAATTTGTTTAAAGGATG 57.130 30.769 0.00 0.00 41.15 3.51
2540 2626 7.925483 TGACAAGTGAATTTGTTTAAAGGATGG 59.075 33.333 0.00 0.00 41.15 3.51
2541 2627 8.017418 ACAAGTGAATTTGTTTAAAGGATGGA 57.983 30.769 0.00 0.00 38.05 3.41
2542 2628 8.482128 ACAAGTGAATTTGTTTAAAGGATGGAA 58.518 29.630 0.00 0.00 38.05 3.53
2543 2629 9.323985 CAAGTGAATTTGTTTAAAGGATGGAAA 57.676 29.630 0.00 0.00 0.00 3.13
2544 2630 9.898152 AAGTGAATTTGTTTAAAGGATGGAAAA 57.102 25.926 0.00 0.00 0.00 2.29
2545 2631 9.898152 AGTGAATTTGTTTAAAGGATGGAAAAA 57.102 25.926 0.00 0.00 0.00 1.94
2546 2632 9.929722 GTGAATTTGTTTAAAGGATGGAAAAAC 57.070 29.630 0.00 0.00 0.00 2.43
2547 2633 9.898152 TGAATTTGTTTAAAGGATGGAAAAACT 57.102 25.926 0.00 0.00 32.57 2.66
2550 2636 9.898152 ATTTGTTTAAAGGATGGAAAAACTTGA 57.102 25.926 0.00 0.00 32.57 3.02
2551 2637 9.726438 TTTGTTTAAAGGATGGAAAAACTTGAA 57.274 25.926 0.00 0.00 32.57 2.69
2552 2638 8.710835 TGTTTAAAGGATGGAAAAACTTGAAC 57.289 30.769 0.00 0.00 32.57 3.18
2553 2639 8.536175 TGTTTAAAGGATGGAAAAACTTGAACT 58.464 29.630 0.00 0.00 32.57 3.01
2557 2643 7.654022 AAGGATGGAAAAACTTGAACTAACA 57.346 32.000 0.00 0.00 0.00 2.41
2558 2644 7.839680 AGGATGGAAAAACTTGAACTAACAT 57.160 32.000 0.00 0.00 0.00 2.71
2559 2645 8.934023 AGGATGGAAAAACTTGAACTAACATA 57.066 30.769 0.00 0.00 0.00 2.29
2560 2646 9.533831 AGGATGGAAAAACTTGAACTAACATAT 57.466 29.630 0.00 0.00 0.00 1.78
2585 2671 9.768215 ATTTTCCAAGAAGTATTTAGGAATGGA 57.232 29.630 0.00 0.00 34.26 3.41
2586 2672 8.807948 TTTCCAAGAAGTATTTAGGAATGGAG 57.192 34.615 0.00 0.00 35.97 3.86
2587 2673 6.900194 TCCAAGAAGTATTTAGGAATGGAGG 58.100 40.000 0.00 0.00 31.26 4.30
2588 2674 6.676632 TCCAAGAAGTATTTAGGAATGGAGGA 59.323 38.462 0.00 0.00 31.26 3.71
2589 2675 7.183839 TCCAAGAAGTATTTAGGAATGGAGGAA 59.816 37.037 0.00 0.00 31.26 3.36
2590 2676 8.001292 CCAAGAAGTATTTAGGAATGGAGGAAT 58.999 37.037 0.00 0.00 0.00 3.01
2591 2677 8.844244 CAAGAAGTATTTAGGAATGGAGGAATG 58.156 37.037 0.00 0.00 0.00 2.67
2592 2678 7.521669 AGAAGTATTTAGGAATGGAGGAATGG 58.478 38.462 0.00 0.00 0.00 3.16
2593 2679 7.350921 AGAAGTATTTAGGAATGGAGGAATGGA 59.649 37.037 0.00 0.00 0.00 3.41
2594 2680 7.084268 AGTATTTAGGAATGGAGGAATGGAG 57.916 40.000 0.00 0.00 0.00 3.86
2595 2681 6.621514 AGTATTTAGGAATGGAGGAATGGAGT 59.378 38.462 0.00 0.00 0.00 3.85
2596 2682 7.794683 AGTATTTAGGAATGGAGGAATGGAGTA 59.205 37.037 0.00 0.00 0.00 2.59
2597 2683 7.654287 ATTTAGGAATGGAGGAATGGAGTAT 57.346 36.000 0.00 0.00 0.00 2.12
2598 2684 7.465900 TTTAGGAATGGAGGAATGGAGTATT 57.534 36.000 0.00 0.00 0.00 1.89
2599 2685 8.575736 TTTAGGAATGGAGGAATGGAGTATTA 57.424 34.615 0.00 0.00 0.00 0.98
2600 2686 6.694445 AGGAATGGAGGAATGGAGTATTAG 57.306 41.667 0.00 0.00 0.00 1.73
2601 2687 6.393897 AGGAATGGAGGAATGGAGTATTAGA 58.606 40.000 0.00 0.00 0.00 2.10
2665 2754 5.164012 TGACAAGTGAATTTGTTTTTGCACG 60.164 36.000 0.00 0.00 41.15 5.34
2704 2817 3.924144 GCACCCAACTATGCAATCAAAA 58.076 40.909 0.00 0.00 41.65 2.44
2837 2954 5.073144 TGACTGAATCTGTACCTTTTCCCTT 59.927 40.000 0.00 0.00 0.00 3.95
2839 2956 6.373759 ACTGAATCTGTACCTTTTCCCTTTT 58.626 36.000 0.00 0.00 0.00 2.27
2876 2994 4.159506 GGCTATTCATTTGCCAACCACTTA 59.840 41.667 0.00 0.00 45.46 2.24
2982 3102 3.677148 CGGCACTATTCTTCAGCTTCTGA 60.677 47.826 0.00 0.00 38.87 3.27
2983 3103 3.870419 GGCACTATTCTTCAGCTTCTGAG 59.130 47.826 0.00 0.00 41.75 3.35
3223 3525 2.780643 CTGCTCGGTCATGTTGCG 59.219 61.111 0.00 0.00 0.00 4.85
3263 3565 2.943827 TTGGGTGGCCTGGGCATA 60.944 61.111 26.61 12.93 44.11 3.14
3300 3602 0.106149 GAACTGGTCGTTGAGGGTGT 59.894 55.000 0.00 0.00 35.56 4.16
3319 3621 0.541530 TGCTGGCCTTGGTTGCAATA 60.542 50.000 0.59 0.00 0.00 1.90
3441 3747 1.349357 AGCAAACCCTCTTCTGGACTC 59.651 52.381 0.00 0.00 0.00 3.36
3442 3748 1.349357 GCAAACCCTCTTCTGGACTCT 59.651 52.381 0.00 0.00 0.00 3.24
3522 3828 0.833287 GCTCAAGGCTAGGACCATCA 59.167 55.000 0.00 0.00 38.06 3.07
3542 4313 1.153978 CGCGATGCTGCACCAAAAT 60.154 52.632 3.57 0.00 34.15 1.82
3556 4327 1.392589 CAAAATCGGTGGATCCAGGG 58.607 55.000 16.81 10.31 35.57 4.45
3651 4824 4.213270 TGAAGTTATCGACCAGCTTGTTTG 59.787 41.667 3.16 0.00 0.00 2.93
3715 4888 3.392769 CAAAATCATTTTGCCGGCATG 57.607 42.857 33.25 25.87 42.91 4.06
3717 4890 0.903942 AATCATTTTGCCGGCATGGT 59.096 45.000 33.25 20.18 41.21 3.55
3726 4899 2.279517 CGGCATGGTCTAGTCGCC 60.280 66.667 0.00 0.00 39.45 5.54
3748 4921 1.515521 CCTGGAACTCAACGTTGGGC 61.516 60.000 27.79 12.48 35.56 5.36
3758 4931 3.977244 CGTTGGGCTGTTGGGTGC 61.977 66.667 0.00 0.00 0.00 5.01
3763 4936 2.736531 GGCTGTTGGGTGCCTTTG 59.263 61.111 0.00 0.00 45.26 2.77
3764 4937 1.832167 GGCTGTTGGGTGCCTTTGA 60.832 57.895 0.00 0.00 45.26 2.69
3765 4938 1.398958 GGCTGTTGGGTGCCTTTGAA 61.399 55.000 0.00 0.00 45.26 2.69
3773 4949 2.172293 TGGGTGCCTTTGAAAGCAAAAT 59.828 40.909 0.00 0.00 42.96 1.82
3808 4985 3.055719 CGCAAACCGGTGCTGGAT 61.056 61.111 8.52 0.00 42.62 3.41
3846 5023 0.535335 GCGACAGTTGGATCACCCTA 59.465 55.000 0.00 0.00 35.38 3.53
3908 5085 4.688879 CACTTGTTGTCCGAGTATGCTTTA 59.311 41.667 0.00 0.00 35.47 1.85
3968 5145 1.633432 CTTCAGACCATTACCCACCCA 59.367 52.381 0.00 0.00 0.00 4.51
3969 5146 1.748732 TCAGACCATTACCCACCCAA 58.251 50.000 0.00 0.00 0.00 4.12
4001 5178 9.965902 ATATATCAGTTTCTTGACTGGTTTCTT 57.034 29.630 5.31 0.00 45.54 2.52
4006 5183 3.746045 TCTTGACTGGTTTCTTAGCGT 57.254 42.857 0.00 0.00 0.00 5.07
4076 5253 4.235762 ACGTTGTGGCGGCTCTGT 62.236 61.111 11.43 4.50 35.98 3.41
4078 5255 1.447838 CGTTGTGGCGGCTCTGTAT 60.448 57.895 11.43 0.00 0.00 2.29
4107 5284 2.224606 ACTCATGTGTGTTTGGCTGAG 58.775 47.619 0.00 0.00 36.92 3.35
4126 5303 0.250640 GCTGCCTGCATAGCCAGTAT 60.251 55.000 6.42 0.00 42.31 2.12
4194 5371 0.601311 GCGAAGTGTGCTGAGAAGGT 60.601 55.000 0.00 0.00 0.00 3.50
4214 5391 2.300437 GTTCCTTCTGCACACTAGACCT 59.700 50.000 0.00 0.00 0.00 3.85
4292 5469 4.957296 TCAGTGTGTTTTCTAGGTTCTCC 58.043 43.478 0.00 0.00 0.00 3.71
4298 5475 3.135167 TGTTTTCTAGGTTCTCCGGTTGT 59.865 43.478 0.00 0.00 39.05 3.32
4317 5494 5.182380 GGTTGTCTTCGGTTTCCATTTCATA 59.818 40.000 0.00 0.00 0.00 2.15
4357 5534 2.526304 TCTGTTTCGCTTGCTGTACT 57.474 45.000 0.00 0.00 0.00 2.73
4363 5540 2.399396 TCGCTTGCTGTACTTTTTGC 57.601 45.000 0.00 0.00 0.00 3.68
4364 5541 1.946768 TCGCTTGCTGTACTTTTTGCT 59.053 42.857 0.00 0.00 0.00 3.91
4409 5588 9.114952 TGAAAGTGACACAATTAGTTGTATTCA 57.885 29.630 8.59 6.85 46.49 2.57
4410 5589 9.944663 GAAAGTGACACAATTAGTTGTATTCAA 57.055 29.630 8.59 0.00 46.49 2.69
4412 5591 8.099364 AGTGACACAATTAGTTGTATTCAAGG 57.901 34.615 8.59 0.31 46.49 3.61
4413 5592 7.936847 AGTGACACAATTAGTTGTATTCAAGGA 59.063 33.333 8.59 0.00 46.49 3.36
4462 5645 9.678260 AGTTCAATCTAAGTGCATCTAAGAATT 57.322 29.630 0.00 0.00 0.00 2.17
4581 5911 1.625818 GGAGGTCGGGAGATATTGCAT 59.374 52.381 0.00 0.00 43.27 3.96
4677 6007 4.969484 AGAAAACTCGAAAAGCCCTTCTA 58.031 39.130 0.00 0.00 0.00 2.10
4815 6157 4.040755 ACCTGGACTAGTATTCATGGCTT 58.959 43.478 0.00 0.00 0.00 4.35
4882 6224 3.392595 GATGCAACTGCTCCGCTGC 62.393 63.158 2.95 0.00 42.66 5.25
5154 6497 5.750067 TCCAGTATTTTTCTATACGTTCGGC 59.250 40.000 0.00 0.00 36.37 5.54
5207 6570 5.995282 TGGACTGTACATGAAACAACTAAGG 59.005 40.000 0.00 0.00 0.00 2.69
5214 6577 0.879090 GAAACAACTAAGGGGTGGCG 59.121 55.000 0.00 0.00 36.85 5.69
5223 6586 2.124151 GGGGTGGCGAATCATGCT 60.124 61.111 0.00 0.00 0.00 3.79
5335 6698 0.310854 GAACTGGCAAAGGACAACGG 59.689 55.000 0.00 0.00 0.00 4.44
5359 6722 1.747924 CGAGAGTGGAGCTGAGAATGA 59.252 52.381 0.00 0.00 0.00 2.57
5630 6993 2.549754 CCGACTGAAAATTGTGAGCAGT 59.450 45.455 0.00 0.00 42.03 4.40
5631 6994 3.003689 CCGACTGAAAATTGTGAGCAGTT 59.996 43.478 0.00 0.00 39.68 3.16
6315 7682 7.505585 TCATTTCTACCCTCAACAGTTTGATTT 59.494 33.333 0.00 0.00 41.05 2.17
6357 7724 4.243008 TTCCTCGCCGTGCACCAA 62.243 61.111 12.15 0.00 0.00 3.67
6502 7879 2.972505 CGCCCCATGTCCGCATAC 60.973 66.667 0.00 0.00 33.30 2.39
6613 8874 5.738909 AGAAAGACTTGGTGATACTCCATG 58.261 41.667 0.00 0.00 34.75 3.66
6626 8887 2.573369 ACTCCATGCATGATCAAGAGC 58.427 47.619 28.31 5.31 0.00 4.09
6650 8911 3.753272 GCAGAGCAGTAAATCAAGTTGGA 59.247 43.478 2.34 0.00 0.00 3.53
6654 8915 4.144297 AGCAGTAAATCAAGTTGGAGCAA 58.856 39.130 2.34 0.00 0.00 3.91
6782 9043 6.432472 AGATGAACTTTGACCTGAATTTCTCC 59.568 38.462 0.00 0.00 0.00 3.71
6807 9068 6.928582 CCACCTGGAGAAGATGAGGATCAAT 61.929 48.000 0.00 0.00 44.09 2.57
6824 9085 5.221009 GGATCAATCTGTGGCAAAGAAGATC 60.221 44.000 28.29 28.29 37.92 2.75
7036 9297 9.703892 ATGCACTTAAGTGTTAAAATGCATTAA 57.296 25.926 30.90 0.90 45.82 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 2.616376 CACCAACGATTTTCTGGACACA 59.384 45.455 0.00 0.00 34.16 3.72
414 415 1.522092 CCACGAGGCCTATGCAGAA 59.478 57.895 4.42 0.00 40.13 3.02
648 661 1.812571 CAGGCAAATACGTTCTGGCTT 59.187 47.619 14.84 0.22 42.79 4.35
701 715 5.221224 CCAAAGCAACTGACAACCAGATTTA 60.221 40.000 0.00 0.00 45.78 1.40
721 735 3.765381 TGGAGCAATCACAAGATCCAAA 58.235 40.909 0.00 0.00 46.32 3.28
912 927 3.493503 CAGAACCACCTTCGTACTTGTTC 59.506 47.826 0.00 0.00 33.60 3.18
918 933 0.034337 TGCCAGAACCACCTTCGTAC 59.966 55.000 0.00 0.00 33.60 3.67
1015 1034 7.576477 GCAAAGAAGAAGAACAAGGATTAGCAT 60.576 37.037 0.00 0.00 0.00 3.79
1066 1085 1.614413 CTCCGGTCTTAGCCATAGGAC 59.386 57.143 0.00 0.00 37.30 3.85
1091 1110 2.224621 TGCCTTCTCAACCTCTTCCTTG 60.225 50.000 0.00 0.00 0.00 3.61
1116 1135 0.178873 TAGGCTTGGGACCCTTCACT 60.179 55.000 13.00 7.76 32.65 3.41
1153 1172 2.545946 GGATACGCTTCATCTCTTTGGC 59.454 50.000 0.00 0.00 0.00 4.52
1279 1298 8.565416 CATAGCAAGATCATAGCATCAAAAGAA 58.435 33.333 0.00 0.00 0.00 2.52
1308 1327 6.016860 GCATCAGCCTGAAATATTCACATACA 60.017 38.462 0.00 0.00 35.46 2.29
1394 1414 3.089284 GGAACTGATTCGTGGGGAAAAT 58.911 45.455 0.00 0.00 38.36 1.82
1555 1583 5.008019 CACTAGAAAAATGCGACATAGCCAT 59.992 40.000 0.00 0.00 36.02 4.40
1562 1590 5.295787 ACAAACTCACTAGAAAAATGCGACA 59.704 36.000 0.00 0.00 0.00 4.35
1563 1591 5.748592 ACAAACTCACTAGAAAAATGCGAC 58.251 37.500 0.00 0.00 0.00 5.19
1671 1702 7.886629 ATGTGCCTAAGATTATGACAAATGT 57.113 32.000 0.00 0.00 0.00 2.71
1672 1703 9.888878 CTAATGTGCCTAAGATTATGACAAATG 57.111 33.333 0.00 0.00 0.00 2.32
1998 2070 4.525912 TTGTAAACGGAGGGAGTACTTC 57.474 45.455 0.00 0.00 0.00 3.01
2059 2131 4.092529 TGAACAAACACACTAAAACGCGTA 59.907 37.500 14.46 0.00 0.00 4.42
2062 2134 4.408694 AGTGAACAAACACACTAAAACGC 58.591 39.130 0.00 0.00 44.06 4.84
2125 2200 6.522054 TCCCTCCGTTCACAAATATAAGATC 58.478 40.000 0.00 0.00 0.00 2.75
2142 2217 4.682778 TGGAAAATATGTACTCCCTCCG 57.317 45.455 0.00 0.00 0.00 4.63
2278 2363 6.708949 GCAAGGATACGGGATTCAACTATTTA 59.291 38.462 0.00 0.00 46.39 1.40
2329 2414 2.922740 AAGACGTCAGGGCAGTTTAA 57.077 45.000 19.50 0.00 0.00 1.52
2330 2415 5.128171 ACATATAAGACGTCAGGGCAGTTTA 59.872 40.000 19.50 5.23 0.00 2.01
2331 2416 4.081087 ACATATAAGACGTCAGGGCAGTTT 60.081 41.667 19.50 2.90 0.00 2.66
2332 2417 3.451178 ACATATAAGACGTCAGGGCAGTT 59.549 43.478 19.50 3.68 0.00 3.16
2333 2418 3.031736 ACATATAAGACGTCAGGGCAGT 58.968 45.455 19.50 6.59 0.00 4.40
2334 2419 3.735237 ACATATAAGACGTCAGGGCAG 57.265 47.619 19.50 5.93 0.00 4.85
2336 2421 3.825014 TCCTACATATAAGACGTCAGGGC 59.175 47.826 19.50 0.00 0.00 5.19
2339 2424 7.215719 TCCATTCCTACATATAAGACGTCAG 57.784 40.000 19.50 3.20 0.00 3.51
2340 2425 6.208797 CCTCCATTCCTACATATAAGACGTCA 59.791 42.308 19.50 0.00 0.00 4.35
2341 2426 6.208994 ACCTCCATTCCTACATATAAGACGTC 59.791 42.308 7.70 7.70 0.00 4.34
2342 2427 6.075984 ACCTCCATTCCTACATATAAGACGT 58.924 40.000 0.00 0.00 0.00 4.34
2343 2428 6.591750 ACCTCCATTCCTACATATAAGACG 57.408 41.667 0.00 0.00 0.00 4.18
2344 2429 8.653036 ACTACCTCCATTCCTACATATAAGAC 57.347 38.462 0.00 0.00 0.00 3.01
2345 2430 9.976776 CTACTACCTCCATTCCTACATATAAGA 57.023 37.037 0.00 0.00 0.00 2.10
2346 2431 9.976776 TCTACTACCTCCATTCCTACATATAAG 57.023 37.037 0.00 0.00 0.00 1.73
2350 2435 9.125255 ACTATCTACTACCTCCATTCCTACATA 57.875 37.037 0.00 0.00 0.00 2.29
2351 2436 8.002431 ACTATCTACTACCTCCATTCCTACAT 57.998 38.462 0.00 0.00 0.00 2.29
2352 2437 7.295196 AGACTATCTACTACCTCCATTCCTACA 59.705 40.741 0.00 0.00 0.00 2.74
2353 2438 7.692172 AGACTATCTACTACCTCCATTCCTAC 58.308 42.308 0.00 0.00 0.00 3.18
2354 2439 7.891825 AGACTATCTACTACCTCCATTCCTA 57.108 40.000 0.00 0.00 0.00 2.94
2355 2440 6.790177 AGACTATCTACTACCTCCATTCCT 57.210 41.667 0.00 0.00 0.00 3.36
2392 2477 8.247562 TGCATTGTCCATAAAAGTATTTGGTAC 58.752 33.333 0.00 0.00 39.02 3.34
2402 2487 4.160065 TGGTGGATGCATTGTCCATAAAAG 59.840 41.667 10.63 0.00 46.68 2.27
2415 2500 1.078497 CTTAGCGGTGGTGGATGCA 60.078 57.895 0.00 0.00 0.00 3.96
2418 2503 0.676782 GCAACTTAGCGGTGGTGGAT 60.677 55.000 0.00 0.00 0.00 3.41
2428 2513 4.292977 ACACACTTGAAAGCAACTTAGC 57.707 40.909 0.00 0.00 0.00 3.09
2466 2552 5.520376 AACAAATTCACTTGTCAAGGGAG 57.480 39.130 16.86 8.67 42.92 4.30
2468 2554 6.675244 GCAAAAACAAATTCACTTGTCAAGGG 60.675 38.462 16.85 13.07 38.59 3.95
2469 2555 6.128336 TGCAAAAACAAATTCACTTGTCAAGG 60.128 34.615 16.85 6.19 38.59 3.61
2470 2556 6.829703 TGCAAAAACAAATTCACTTGTCAAG 58.170 32.000 11.17 11.17 38.59 3.02
2472 2558 6.648310 TCTTGCAAAAACAAATTCACTTGTCA 59.352 30.769 0.00 0.00 38.59 3.58
2473 2559 7.059448 TCTTGCAAAAACAAATTCACTTGTC 57.941 32.000 0.00 0.00 38.59 3.18
2474 2560 7.173047 ACTTCTTGCAAAAACAAATTCACTTGT 59.827 29.630 0.00 0.00 41.31 3.16
2475 2561 7.520686 ACTTCTTGCAAAAACAAATTCACTTG 58.479 30.769 0.00 0.00 0.00 3.16
2476 2562 7.671495 ACTTCTTGCAAAAACAAATTCACTT 57.329 28.000 0.00 0.00 0.00 3.16
2477 2563 8.947055 ATACTTCTTGCAAAAACAAATTCACT 57.053 26.923 0.00 0.00 0.00 3.41
2489 2575 9.912634 CAAGGAAAATCTAATACTTCTTGCAAA 57.087 29.630 0.00 0.00 0.00 3.68
2490 2576 9.295825 TCAAGGAAAATCTAATACTTCTTGCAA 57.704 29.630 0.00 0.00 0.00 4.08
2491 2577 8.730680 GTCAAGGAAAATCTAATACTTCTTGCA 58.269 33.333 0.00 0.00 0.00 4.08
2492 2578 8.730680 TGTCAAGGAAAATCTAATACTTCTTGC 58.269 33.333 0.00 0.00 0.00 4.01
2497 2583 9.793259 TCACTTGTCAAGGAAAATCTAATACTT 57.207 29.630 16.85 0.00 0.00 2.24
2498 2584 9.793259 TTCACTTGTCAAGGAAAATCTAATACT 57.207 29.630 16.85 0.00 0.00 2.12
2502 2588 9.748708 CAAATTCACTTGTCAAGGAAAATCTAA 57.251 29.630 16.85 0.42 0.00 2.10
2503 2589 8.912988 ACAAATTCACTTGTCAAGGAAAATCTA 58.087 29.630 16.85 0.00 34.37 1.98
2504 2590 7.785033 ACAAATTCACTTGTCAAGGAAAATCT 58.215 30.769 16.85 0.00 34.37 2.40
2505 2591 8.424274 AACAAATTCACTTGTCAAGGAAAATC 57.576 30.769 16.85 0.00 38.59 2.17
2506 2592 8.791327 AAACAAATTCACTTGTCAAGGAAAAT 57.209 26.923 16.85 9.76 38.59 1.82
2507 2593 9.712305 TTAAACAAATTCACTTGTCAAGGAAAA 57.288 25.926 16.85 8.01 38.59 2.29
2508 2594 9.712305 TTTAAACAAATTCACTTGTCAAGGAAA 57.288 25.926 16.85 10.30 38.59 3.13
2509 2595 9.364989 CTTTAAACAAATTCACTTGTCAAGGAA 57.635 29.630 16.85 15.66 38.59 3.36
2510 2596 7.978975 CCTTTAAACAAATTCACTTGTCAAGGA 59.021 33.333 16.85 8.33 39.94 3.36
2511 2597 7.978975 TCCTTTAAACAAATTCACTTGTCAAGG 59.021 33.333 16.85 6.19 38.59 3.61
2512 2598 8.925161 TCCTTTAAACAAATTCACTTGTCAAG 57.075 30.769 11.17 11.17 38.59 3.02
2513 2599 9.311916 CATCCTTTAAACAAATTCACTTGTCAA 57.688 29.630 0.00 0.00 38.59 3.18
2514 2600 7.925483 CCATCCTTTAAACAAATTCACTTGTCA 59.075 33.333 0.00 0.00 38.59 3.58
2515 2601 8.141268 TCCATCCTTTAAACAAATTCACTTGTC 58.859 33.333 0.00 0.00 38.59 3.18
2516 2602 8.017418 TCCATCCTTTAAACAAATTCACTTGT 57.983 30.769 0.00 0.00 41.31 3.16
2517 2603 8.885494 TTCCATCCTTTAAACAAATTCACTTG 57.115 30.769 0.00 0.00 0.00 3.16
2518 2604 9.898152 TTTTCCATCCTTTAAACAAATTCACTT 57.102 25.926 0.00 0.00 0.00 3.16
2519 2605 9.898152 TTTTTCCATCCTTTAAACAAATTCACT 57.102 25.926 0.00 0.00 0.00 3.41
2520 2606 9.929722 GTTTTTCCATCCTTTAAACAAATTCAC 57.070 29.630 0.00 0.00 0.00 3.18
2521 2607 9.898152 AGTTTTTCCATCCTTTAAACAAATTCA 57.102 25.926 0.00 0.00 32.58 2.57
2524 2610 9.898152 TCAAGTTTTTCCATCCTTTAAACAAAT 57.102 25.926 0.00 0.00 32.58 2.32
2525 2611 9.726438 TTCAAGTTTTTCCATCCTTTAAACAAA 57.274 25.926 0.00 0.00 32.58 2.83
2526 2612 9.157104 GTTCAAGTTTTTCCATCCTTTAAACAA 57.843 29.630 0.00 0.00 32.58 2.83
2527 2613 8.536175 AGTTCAAGTTTTTCCATCCTTTAAACA 58.464 29.630 0.00 0.00 32.58 2.83
2528 2614 8.942338 AGTTCAAGTTTTTCCATCCTTTAAAC 57.058 30.769 0.00 0.00 0.00 2.01
2531 2617 9.191479 TGTTAGTTCAAGTTTTTCCATCCTTTA 57.809 29.630 0.00 0.00 0.00 1.85
2532 2618 8.073467 TGTTAGTTCAAGTTTTTCCATCCTTT 57.927 30.769 0.00 0.00 0.00 3.11
2533 2619 7.654022 TGTTAGTTCAAGTTTTTCCATCCTT 57.346 32.000 0.00 0.00 0.00 3.36
2534 2620 7.839680 ATGTTAGTTCAAGTTTTTCCATCCT 57.160 32.000 0.00 0.00 0.00 3.24
2559 2645 9.768215 TCCATTCCTAAATACTTCTTGGAAAAT 57.232 29.630 0.00 0.00 37.18 1.82
2560 2646 9.243105 CTCCATTCCTAAATACTTCTTGGAAAA 57.757 33.333 0.00 0.00 37.18 2.29
2561 2647 7.834181 CCTCCATTCCTAAATACTTCTTGGAAA 59.166 37.037 0.00 0.00 37.18 3.13
2562 2648 7.183839 TCCTCCATTCCTAAATACTTCTTGGAA 59.816 37.037 0.00 0.00 37.87 3.53
2563 2649 6.676632 TCCTCCATTCCTAAATACTTCTTGGA 59.323 38.462 0.00 0.00 0.00 3.53
2564 2650 6.900194 TCCTCCATTCCTAAATACTTCTTGG 58.100 40.000 0.00 0.00 0.00 3.61
2565 2651 8.844244 CATTCCTCCATTCCTAAATACTTCTTG 58.156 37.037 0.00 0.00 0.00 3.02
2566 2652 8.001292 CCATTCCTCCATTCCTAAATACTTCTT 58.999 37.037 0.00 0.00 0.00 2.52
2567 2653 7.350921 TCCATTCCTCCATTCCTAAATACTTCT 59.649 37.037 0.00 0.00 0.00 2.85
2568 2654 7.518188 TCCATTCCTCCATTCCTAAATACTTC 58.482 38.462 0.00 0.00 0.00 3.01
2569 2655 7.129504 ACTCCATTCCTCCATTCCTAAATACTT 59.870 37.037 0.00 0.00 0.00 2.24
2570 2656 6.621514 ACTCCATTCCTCCATTCCTAAATACT 59.378 38.462 0.00 0.00 0.00 2.12
2571 2657 6.842676 ACTCCATTCCTCCATTCCTAAATAC 58.157 40.000 0.00 0.00 0.00 1.89
2572 2658 8.757307 ATACTCCATTCCTCCATTCCTAAATA 57.243 34.615 0.00 0.00 0.00 1.40
2573 2659 7.654287 ATACTCCATTCCTCCATTCCTAAAT 57.346 36.000 0.00 0.00 0.00 1.40
2574 2660 7.465900 AATACTCCATTCCTCCATTCCTAAA 57.534 36.000 0.00 0.00 0.00 1.85
2575 2661 8.016652 TCTAATACTCCATTCCTCCATTCCTAA 58.983 37.037 0.00 0.00 0.00 2.69
2576 2662 7.544650 TCTAATACTCCATTCCTCCATTCCTA 58.455 38.462 0.00 0.00 0.00 2.94
2577 2663 6.393897 TCTAATACTCCATTCCTCCATTCCT 58.606 40.000 0.00 0.00 0.00 3.36
2578 2664 6.688073 TCTAATACTCCATTCCTCCATTCC 57.312 41.667 0.00 0.00 0.00 3.01
2579 2665 9.579932 AAAATCTAATACTCCATTCCTCCATTC 57.420 33.333 0.00 0.00 0.00 2.67
2580 2666 9.942526 AAAAATCTAATACTCCATTCCTCCATT 57.057 29.630 0.00 0.00 0.00 3.16
2582 2668 9.847224 GTAAAAATCTAATACTCCATTCCTCCA 57.153 33.333 0.00 0.00 0.00 3.86
2583 2669 9.847224 TGTAAAAATCTAATACTCCATTCCTCC 57.153 33.333 0.00 0.00 0.00 4.30
2628 2714 3.070159 TCACTTGTCAAGGGAGAGTTGAG 59.930 47.826 13.72 0.00 35.61 3.02
2629 2715 3.038280 TCACTTGTCAAGGGAGAGTTGA 58.962 45.455 13.72 4.73 35.61 3.18
2630 2716 3.475566 TCACTTGTCAAGGGAGAGTTG 57.524 47.619 13.72 2.36 35.61 3.16
2665 2754 2.096496 GTGCACACAGTCATGGCTTATC 59.904 50.000 13.17 0.00 0.00 1.75
2698 2811 6.998074 TGACAGAGGTAAGTGAATGTTTTGAT 59.002 34.615 0.00 0.00 0.00 2.57
2704 2817 6.772716 ACAAAATGACAGAGGTAAGTGAATGT 59.227 34.615 0.00 0.00 0.00 2.71
2839 2956 5.016051 TGAATAGCCTTGCAACACAAAAA 57.984 34.783 0.00 0.00 37.96 1.94
2982 3102 2.807247 GTGCCACACCAAAGGTTCT 58.193 52.632 0.00 0.00 31.02 3.01
3159 3460 1.004044 CATCCAACAGAAGCTCCCTGT 59.996 52.381 13.96 13.96 45.88 4.00
3223 3525 4.040952 ACTCAATAGGGTGGCAGATATCAC 59.959 45.833 5.32 0.00 0.00 3.06
3263 3565 2.879026 GTTCGCCTTTCTCAGGTCTTTT 59.121 45.455 0.00 0.00 46.07 2.27
3300 3602 0.541530 TATTGCAACCAAGGCCAGCA 60.542 50.000 5.01 1.84 33.80 4.41
3319 3621 1.428869 AGGTTGAGAGGTGTCAGCTT 58.571 50.000 5.91 0.00 0.00 3.74
3380 3682 2.584391 GGAGGCCGTGTGGAGAAGT 61.584 63.158 0.00 0.00 37.49 3.01
3441 3747 2.801631 GCCCTCCGGTCCATCTGAG 61.802 68.421 0.00 0.00 0.00 3.35
3442 3748 2.764128 GCCCTCCGGTCCATCTGA 60.764 66.667 0.00 0.00 0.00 3.27
3542 4313 2.366837 ATGCCCTGGATCCACCGA 60.367 61.111 11.44 0.00 42.61 4.69
3556 4327 2.681848 ACATTTAGTGCTCAGCTGATGC 59.318 45.455 18.63 21.54 40.05 3.91
3585 4748 6.247676 TCACCAGATGAAGAAATTCCATCAA 58.752 36.000 12.47 0.00 39.18 2.57
3613 4786 6.645827 CGATAACTTCAGAGTCGAGGTCTATA 59.354 42.308 0.00 0.00 34.21 1.31
3673 4846 2.695314 GGCTGATTTGGCCGAGTAG 58.305 57.895 0.00 0.00 40.19 2.57
3714 4887 4.753662 AGGCCGGCGACTAGACCA 62.754 66.667 22.54 0.00 0.00 4.02
3715 4888 4.208686 CAGGCCGGCGACTAGACC 62.209 72.222 22.54 3.21 0.00 3.85
3717 4890 3.949885 TTCCAGGCCGGCGACTAGA 62.950 63.158 22.54 8.66 33.14 2.43
3726 4899 1.597027 AACGTTGAGTTCCAGGCCG 60.597 57.895 0.00 0.00 39.16 6.13
3748 4921 1.538849 GCTTTCAAAGGCACCCAACAG 60.539 52.381 0.00 0.00 0.00 3.16
3758 4931 3.559242 TGCGGAAATTTTGCTTTCAAAGG 59.441 39.130 14.85 0.00 42.50 3.11
3759 4932 4.792528 TGCGGAAATTTTGCTTTCAAAG 57.207 36.364 14.85 0.00 42.50 2.77
3760 4933 4.024218 CCATGCGGAAATTTTGCTTTCAAA 60.024 37.500 14.85 0.00 40.17 2.69
3761 4934 3.497640 CCATGCGGAAATTTTGCTTTCAA 59.502 39.130 14.85 0.00 36.95 2.69
3763 4936 3.066380 ACCATGCGGAAATTTTGCTTTC 58.934 40.909 14.85 0.00 34.95 2.62
3764 4937 3.124578 ACCATGCGGAAATTTTGCTTT 57.875 38.095 14.85 3.42 35.59 3.51
3765 4938 2.807392 CAACCATGCGGAAATTTTGCTT 59.193 40.909 14.85 7.97 35.59 3.91
3773 4949 2.622011 GCGACCAACCATGCGGAAA 61.622 57.895 1.45 0.00 35.59 3.13
3808 4985 2.816672 CGCCTCACTAGATGATCTGCTA 59.183 50.000 4.96 0.00 36.48 3.49
3823 5000 0.037326 GTGATCCAACTGTCGCCTCA 60.037 55.000 0.00 0.00 0.00 3.86
3959 5136 4.417183 TGATATATGGCTTTTGGGTGGGTA 59.583 41.667 0.00 0.00 0.00 3.69
3968 5145 8.814038 AGTCAAGAAACTGATATATGGCTTTT 57.186 30.769 0.00 0.00 0.00 2.27
4001 5178 3.052620 GACTCGCTCTGCCACGCTA 62.053 63.158 0.00 0.00 0.00 4.26
4006 5183 4.426112 CGCTGACTCGCTCTGCCA 62.426 66.667 6.32 0.00 40.01 4.92
4045 5222 2.987149 CACAACGTCTACATGAGTGACC 59.013 50.000 0.00 0.00 0.00 4.02
4076 5253 7.817478 CCAAACACACATGAGTTCTACAGTATA 59.183 37.037 0.00 0.00 0.00 1.47
4078 5255 5.989168 CCAAACACACATGAGTTCTACAGTA 59.011 40.000 0.00 0.00 0.00 2.74
4176 5353 1.795286 GAACCTTCTCAGCACACTTCG 59.205 52.381 0.00 0.00 0.00 3.79
4194 5371 2.563179 GAGGTCTAGTGTGCAGAAGGAA 59.437 50.000 0.00 0.00 0.00 3.36
4206 5383 3.767309 AGAACCATCTGGAGGTCTAGT 57.233 47.619 2.55 0.00 38.76 2.57
4214 5391 0.830648 CGGCCTAAGAACCATCTGGA 59.169 55.000 0.00 0.00 35.59 3.86
4292 5469 1.519408 ATGGAAACCGAAGACAACCG 58.481 50.000 0.00 0.00 0.00 4.44
4298 5475 6.346096 CCTAGTATGAAATGGAAACCGAAGA 58.654 40.000 0.00 0.00 0.00 2.87
4317 5494 6.012771 ACAGAAAACATTTACCTAGGCCTAGT 60.013 38.462 33.00 23.91 0.00 2.57
4357 5534 6.036577 AGAAAGGTGTCAAGAAAGCAAAAA 57.963 33.333 0.00 0.00 0.00 1.94
4429 5612 4.627035 TGCACTTAGATTGAACTGACATCG 59.373 41.667 0.00 0.00 0.00 3.84
4501 5684 8.547967 TCATACTTTCAGTTACTTCCATGTTC 57.452 34.615 0.00 0.00 0.00 3.18
4581 5911 2.189594 CCATGTCTGGCTGAGAAACA 57.810 50.000 0.00 0.00 35.23 2.83
4677 6007 1.274591 ACCGTAAATAACCCTCCCCCT 60.275 52.381 0.00 0.00 0.00 4.79
4815 6157 8.046107 TGCATATATACAGCATTGCATACCTAA 58.954 33.333 11.91 0.00 35.36 2.69
4882 6224 5.033589 AGAATGTTCTCCCATGCTTCTAG 57.966 43.478 0.00 0.00 29.94 2.43
5154 6497 1.216990 ATGCCTTCCTACTTCCCTGG 58.783 55.000 0.00 0.00 0.00 4.45
5207 6570 0.947244 CTAAGCATGATTCGCCACCC 59.053 55.000 0.00 0.00 0.00 4.61
5214 6577 6.691818 CAGCATGAAAGAACTAAGCATGATTC 59.308 38.462 0.00 0.00 39.69 2.52
5223 6586 4.022935 CCTGCAACAGCATGAAAGAACTAA 60.023 41.667 0.00 0.00 39.69 2.24
5335 6698 0.172352 CTCAGCTCCACTCTCGTTCC 59.828 60.000 0.00 0.00 0.00 3.62
5344 6707 0.251354 TGCCTCATTCTCAGCTCCAC 59.749 55.000 0.00 0.00 0.00 4.02
5359 6722 2.567615 AGAAGACCGTTATGAGTTGCCT 59.432 45.455 0.00 0.00 0.00 4.75
5658 7021 7.712797 TGAATAGCAAATACACGATGTCTAGA 58.287 34.615 0.00 0.00 0.00 2.43
5815 7178 1.516386 CACCTGGACGATCGTTCCG 60.516 63.158 23.51 17.06 0.00 4.30
6172 7535 3.197766 TGTTGACTGTCCAAGTTCAGAGT 59.802 43.478 5.17 0.00 40.07 3.24
6315 7682 4.326826 AGCAGGATCGAGACAAATTTGAA 58.673 39.130 24.64 5.04 0.00 2.69
6372 7739 4.865761 GGTGACGCGCCGATGCTA 62.866 66.667 5.73 0.00 34.43 3.49
6387 7754 2.140792 ACTCTGGTCTTGGTGCGGT 61.141 57.895 0.00 0.00 0.00 5.68
6396 7763 2.997897 GCGGGGACACTCTGGTCT 60.998 66.667 0.00 0.00 37.91 3.85
6492 7865 0.249120 CAGGGTGAAGTATGCGGACA 59.751 55.000 0.00 0.00 0.00 4.02
6502 7879 0.617413 ATGAGGTGAGCAGGGTGAAG 59.383 55.000 0.00 0.00 0.00 3.02
6613 8874 1.600013 CTCTGCTGCTCTTGATCATGC 59.400 52.381 0.00 2.50 0.00 4.06
6626 8887 4.379186 CCAACTTGATTTACTGCTCTGCTG 60.379 45.833 0.00 0.00 0.00 4.41
6650 8911 3.551659 GCTTGCTTTACTTCTGCTTTGCT 60.552 43.478 0.00 0.00 0.00 3.91
6654 8915 2.030451 GCTGCTTGCTTTACTTCTGCTT 60.030 45.455 0.00 0.00 38.95 3.91
6782 9043 0.835941 CCTCATCTTCTCCAGGTGGG 59.164 60.000 0.00 0.00 33.08 4.61
6807 9068 4.290711 TGATGATCTTCTTTGCCACAGA 57.709 40.909 9.75 0.00 0.00 3.41
6824 9085 5.095145 TCATCTTCTCCTTCAGGTTGATG 57.905 43.478 0.00 0.00 36.34 3.07


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

AutoCloner maintained by Alex Coulton.