Multiple sequence alignment - TraesCS4D01G270100

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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 TraesCS4D01G270100 chr4D 100.000 2987 0 0 1 2987 441104423 441107409 0.000000e+00 5517.0
1 TraesCS4D01G270100 chr4D 96.933 163 5 0 2392 2554 503794865 503795027 1.050000e-69 274.0
2 TraesCS4D01G270100 chr4B 93.316 1930 62 21 495 2394 547093114 547095006 0.000000e+00 2787.0
3 TraesCS4D01G270100 chr4B 91.480 446 30 7 2545 2987 547094998 547095438 9.160000e-170 606.0
4 TraesCS4D01G270100 chr4B 90.782 358 12 6 1 346 547092613 547092961 2.710000e-125 459.0
5 TraesCS4D01G270100 chr4B 90.667 150 12 2 332 479 547092980 547093129 6.530000e-47 198.0
6 TraesCS4D01G270100 chr4A 89.959 1942 83 63 495 2391 26467018 26465144 0.000000e+00 2403.0
7 TraesCS4D01G270100 chr4A 89.432 511 13 12 1 479 26467504 26467003 9.160000e-170 606.0
8 TraesCS4D01G270100 chr4A 74.440 536 127 9 1355 1885 621009748 621009218 3.880000e-54 222.0
9 TraesCS4D01G270100 chr4A 78.750 320 60 7 1361 1676 26413808 26413493 1.090000e-49 207.0
10 TraesCS4D01G270100 chr4A 83.333 180 27 2 2663 2842 671640682 671640858 2.380000e-36 163.0
11 TraesCS4D01G270100 chr4A 89.744 78 3 3 2564 2636 26465140 26465063 8.810000e-16 95.3
12 TraesCS4D01G270100 chr3D 78.022 546 102 17 1356 1892 157443377 157442841 7.980000e-86 327.0
13 TraesCS4D01G270100 chr3D 75.000 524 100 26 1367 1873 157540561 157540052 2.330000e-51 213.0
14 TraesCS4D01G270100 chr3D 85.143 175 22 4 2668 2841 346309063 346308892 3.060000e-40 176.0
15 TraesCS4D01G270100 chr3D 84.971 173 23 2 2668 2840 481230066 481229897 3.960000e-39 172.0
16 TraesCS4D01G270100 chr3A 77.514 547 106 15 1356 1892 170811690 170812229 2.240000e-81 313.0
17 TraesCS4D01G270100 chr3A 93.421 152 10 0 2393 2544 117808061 117808212 3.000000e-55 226.0
18 TraesCS4D01G270100 chr3A 93.421 152 10 0 2393 2544 117836961 117837112 3.000000e-55 226.0
19 TraesCS4D01G270100 chr3A 86.585 164 19 2 2679 2842 746373921 746374081 8.510000e-41 178.0
20 TraesCS4D01G270100 chr3B 76.881 545 110 15 1356 1892 228690784 228690248 8.100000e-76 294.0
21 TraesCS4D01G270100 chr2D 98.675 151 2 0 2394 2544 247094098 247094248 4.910000e-68 268.0
22 TraesCS4D01G270100 chr2D 84.483 174 24 3 2668 2841 604700921 604700751 5.120000e-38 169.0
23 TraesCS4D01G270100 chr5B 75.382 524 119 9 1355 1873 700997583 700998101 8.270000e-61 244.0
24 TraesCS4D01G270100 chr6A 93.289 149 10 0 2393 2541 568013702 568013850 1.390000e-53 220.0
25 TraesCS4D01G270100 chr7A 90.446 157 14 1 2388 2544 712415718 712415873 3.900000e-49 206.0
26 TraesCS4D01G270100 chr7A 84.000 175 25 3 2668 2842 176271806 176271977 6.620000e-37 165.0
27 TraesCS4D01G270100 chr7D 85.057 174 23 3 2668 2841 41857071 41857241 1.100000e-39 174.0
28 TraesCS4D01G270100 chrUn 82.632 190 27 5 2661 2848 83299846 83300031 2.380000e-36 163.0


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 TraesCS4D01G270100 chr4D 441104423 441107409 2986 False 5517.000000 5517 100.000000 1 2987 1 chr4D.!!$F1 2986
1 TraesCS4D01G270100 chr4B 547092613 547095438 2825 False 1012.500000 2787 91.561250 1 2987 4 chr4B.!!$F1 2986
2 TraesCS4D01G270100 chr4A 26465063 26467504 2441 True 1034.766667 2403 89.711667 1 2636 3 chr4A.!!$R3 2635
3 TraesCS4D01G270100 chr4A 621009218 621009748 530 True 222.000000 222 74.440000 1355 1885 1 chr4A.!!$R2 530
4 TraesCS4D01G270100 chr3D 157442841 157443377 536 True 327.000000 327 78.022000 1356 1892 1 chr3D.!!$R1 536
5 TraesCS4D01G270100 chr3D 157540052 157540561 509 True 213.000000 213 75.000000 1367 1873 1 chr3D.!!$R2 506
6 TraesCS4D01G270100 chr3A 170811690 170812229 539 False 313.000000 313 77.514000 1356 1892 1 chr3A.!!$F3 536
7 TraesCS4D01G270100 chr3B 228690248 228690784 536 True 294.000000 294 76.881000 1356 1892 1 chr3B.!!$R1 536
8 TraesCS4D01G270100 chr5B 700997583 700998101 518 False 244.000000 244 75.382000 1355 1873 1 chr5B.!!$F1 518

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
796 883 0.035725 CTGCAGATCAGCCAGTGGAA 60.036 55.0 15.2 0.0 35.78 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2447 2583 0.098905 CTTGAGATTCGTCGGCTCGA 59.901 55.0 0.0 0.0 38.08 4.04 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
177 193 3.723348 GCGCGCGGGAGAAAAACT 61.723 61.111 33.06 0.00 0.00 2.66
180 196 0.725117 CGCGCGGGAGAAAAACTAAT 59.275 50.000 24.84 0.00 0.00 1.73
191 207 7.355101 GGGAGAAAAACTAATTAATCCTCCCT 58.645 38.462 14.48 1.49 41.58 4.20
306 328 0.249531 TAACAACGAGCGCAAGTGGA 60.250 50.000 11.47 0.00 41.68 4.02
307 329 1.498865 AACAACGAGCGCAAGTGGAG 61.499 55.000 11.47 5.70 41.68 3.86
308 330 1.956170 CAACGAGCGCAAGTGGAGT 60.956 57.895 11.47 0.00 41.68 3.85
365 420 4.436448 GCTGAGCAGCGCGTCAAC 62.436 66.667 8.43 0.00 45.29 3.18
384 439 2.685999 GGCTCAATCCAAGGGGCT 59.314 61.111 0.00 0.00 0.00 5.19
393 448 2.360350 CAAGGGGCTGCATCGTGT 60.360 61.111 0.50 0.00 0.00 4.49
402 457 1.804151 GCTGCATCGTGTTTTGGAGTA 59.196 47.619 0.00 0.00 34.19 2.59
479 540 2.774234 CCAGTAATCCCCATGTGACTCT 59.226 50.000 0.00 0.00 0.00 3.24
480 541 3.200825 CCAGTAATCCCCATGTGACTCTT 59.799 47.826 0.00 0.00 0.00 2.85
481 542 4.446371 CAGTAATCCCCATGTGACTCTTC 58.554 47.826 0.00 0.00 0.00 2.87
482 543 3.456277 AGTAATCCCCATGTGACTCTTCC 59.544 47.826 0.00 0.00 0.00 3.46
484 545 0.119155 TCCCCATGTGACTCTTCCCT 59.881 55.000 0.00 0.00 0.00 4.20
485 546 0.543749 CCCCATGTGACTCTTCCCTC 59.456 60.000 0.00 0.00 0.00 4.30
486 547 1.279496 CCCATGTGACTCTTCCCTCA 58.721 55.000 0.00 0.00 0.00 3.86
487 548 1.630369 CCCATGTGACTCTTCCCTCAA 59.370 52.381 0.00 0.00 0.00 3.02
488 549 2.040278 CCCATGTGACTCTTCCCTCAAA 59.960 50.000 0.00 0.00 0.00 2.69
489 550 3.498481 CCCATGTGACTCTTCCCTCAAAA 60.498 47.826 0.00 0.00 0.00 2.44
490 551 4.144297 CCATGTGACTCTTCCCTCAAAAA 58.856 43.478 0.00 0.00 0.00 1.94
563 624 3.833645 CGCCTCCGGATGGTCGAA 61.834 66.667 20.74 0.00 36.30 3.71
581 642 5.227908 GTCGAACTGGTTTACTTCTGATCA 58.772 41.667 0.00 0.00 0.00 2.92
589 650 8.137437 ACTGGTTTACTTCTGATCAAAATGTTG 58.863 33.333 0.00 0.00 35.95 3.33
626 702 1.676916 CGTACTGTACGTCTCCCTCCA 60.677 57.143 27.27 0.00 46.41 3.86
642 718 4.018506 TCCCTCCAAGCTGATGATTGTTTA 60.019 41.667 0.00 0.00 37.84 2.01
643 719 4.337555 CCCTCCAAGCTGATGATTGTTTAG 59.662 45.833 0.00 0.00 37.84 1.85
645 721 5.065731 CCTCCAAGCTGATGATTGTTTAGTC 59.934 44.000 0.00 0.00 37.84 2.59
646 722 4.631377 TCCAAGCTGATGATTGTTTAGTCG 59.369 41.667 0.00 0.00 37.84 4.18
648 724 5.580691 CCAAGCTGATGATTGTTTAGTCGTA 59.419 40.000 0.00 0.00 37.84 3.43
649 725 6.455646 CCAAGCTGATGATTGTTTAGTCGTAC 60.456 42.308 0.00 0.00 37.84 3.67
650 726 4.798907 AGCTGATGATTGTTTAGTCGTACG 59.201 41.667 9.53 9.53 0.00 3.67
682 769 8.014070 TGATCCCAAATGATTAAGACGTACTA 57.986 34.615 0.00 0.00 0.00 1.82
683 770 7.924412 TGATCCCAAATGATTAAGACGTACTAC 59.076 37.037 0.00 0.00 0.00 2.73
684 771 7.414222 TCCCAAATGATTAAGACGTACTACT 57.586 36.000 0.00 0.00 0.00 2.57
752 839 3.489355 TGCTTGCCAGAGAAGAAAATGA 58.511 40.909 0.00 0.00 0.00 2.57
758 845 5.232463 TGCCAGAGAAGAAAATGAAAATGC 58.768 37.500 0.00 0.00 0.00 3.56
759 846 4.325472 GCCAGAGAAGAAAATGAAAATGCG 59.675 41.667 0.00 0.00 0.00 4.73
760 847 4.860907 CCAGAGAAGAAAATGAAAATGCGG 59.139 41.667 0.00 0.00 0.00 5.69
761 848 4.325472 CAGAGAAGAAAATGAAAATGCGGC 59.675 41.667 0.00 0.00 0.00 6.53
792 879 2.677289 CCCCTGCAGATCAGCCAGT 61.677 63.158 17.39 0.00 41.50 4.00
793 880 1.451567 CCCTGCAGATCAGCCAGTG 60.452 63.158 17.39 0.00 41.50 3.66
794 881 1.451567 CCTGCAGATCAGCCAGTGG 60.452 63.158 17.39 4.20 41.50 4.00
795 882 1.600638 CTGCAGATCAGCCAGTGGA 59.399 57.895 15.20 0.00 35.78 4.02
796 883 0.035725 CTGCAGATCAGCCAGTGGAA 60.036 55.000 15.20 0.00 35.78 3.53
797 884 0.401356 TGCAGATCAGCCAGTGGAAA 59.599 50.000 15.20 0.00 0.00 3.13
798 885 1.005097 TGCAGATCAGCCAGTGGAAAT 59.995 47.619 15.20 1.80 0.00 2.17
799 886 1.404391 GCAGATCAGCCAGTGGAAATG 59.596 52.381 15.20 8.26 0.00 2.32
863 960 0.324943 TGGGCGGGAGAAAAAGAGAG 59.675 55.000 0.00 0.00 0.00 3.20
1035 1153 2.125912 CACTTCACTCGCCTCCCG 60.126 66.667 0.00 0.00 38.61 5.14
1212 1330 2.818132 GACTGGATGAGGGGCTCG 59.182 66.667 0.00 0.00 32.35 5.03
1273 1391 2.607187 GTAAGTGACCATCCACGACTG 58.393 52.381 0.00 0.00 41.67 3.51
1274 1392 0.320771 AAGTGACCATCCACGACTGC 60.321 55.000 0.00 0.00 41.67 4.40
1306 1424 2.867429 AGCGTATTTGCATTGCACTTC 58.133 42.857 11.66 1.89 38.71 3.01
1337 1457 4.378563 CGTGGATATGTACTGATCGAGGAC 60.379 50.000 0.00 1.73 35.80 3.85
1345 1465 2.582498 GATCGAGGACGGCGTTGG 60.582 66.667 16.19 0.00 40.21 3.77
2058 2188 1.198408 CCTTTCCTTTCCGTTTACGCC 59.802 52.381 0.00 0.00 38.18 5.68
2081 2211 3.485947 TTCGATTTCGCATTTGGGAAG 57.514 42.857 9.58 0.79 45.57 3.46
2094 2224 7.175990 TCGCATTTGGGAAGTTAAGTAAGATTT 59.824 33.333 0.00 0.00 33.89 2.17
2353 2489 3.004734 CCATGGTTTCTGACTTTGACCAC 59.995 47.826 2.57 0.00 42.63 4.16
2354 2490 2.650322 TGGTTTCTGACTTTGACCACC 58.350 47.619 0.00 0.00 35.58 4.61
2355 2491 2.025793 TGGTTTCTGACTTTGACCACCA 60.026 45.455 0.00 0.00 35.58 4.17
2403 2539 2.462456 TCTTCACGAAGAGCAATGCT 57.538 45.000 7.79 7.79 42.06 3.79
2404 2540 3.592898 TCTTCACGAAGAGCAATGCTA 57.407 42.857 8.12 0.00 42.06 3.49
2405 2541 4.128925 TCTTCACGAAGAGCAATGCTAT 57.871 40.909 8.12 0.49 42.06 2.97
2406 2542 3.867493 TCTTCACGAAGAGCAATGCTATG 59.133 43.478 8.12 2.20 42.06 2.23
2407 2543 2.554142 TCACGAAGAGCAATGCTATGG 58.446 47.619 8.12 3.52 39.88 2.74
2408 2544 1.600957 CACGAAGAGCAATGCTATGGG 59.399 52.381 8.12 3.12 39.88 4.00
2409 2545 1.233019 CGAAGAGCAATGCTATGGGG 58.767 55.000 8.12 0.00 39.88 4.96
2410 2546 1.202687 CGAAGAGCAATGCTATGGGGA 60.203 52.381 8.12 0.00 39.88 4.81
2411 2547 2.225467 GAAGAGCAATGCTATGGGGAC 58.775 52.381 8.12 0.00 39.88 4.46
2412 2548 0.107456 AGAGCAATGCTATGGGGACG 59.893 55.000 8.12 0.00 39.88 4.79
2413 2549 0.106708 GAGCAATGCTATGGGGACGA 59.893 55.000 8.12 0.00 39.88 4.20
2414 2550 0.179045 AGCAATGCTATGGGGACGAC 60.179 55.000 5.69 0.00 36.99 4.34
2415 2551 0.463654 GCAATGCTATGGGGACGACA 60.464 55.000 0.00 0.00 0.00 4.35
2416 2552 2.016604 GCAATGCTATGGGGACGACAA 61.017 52.381 0.00 0.00 0.00 3.18
2417 2553 2.364632 CAATGCTATGGGGACGACAAA 58.635 47.619 0.00 0.00 0.00 2.83
2418 2554 2.332063 ATGCTATGGGGACGACAAAG 57.668 50.000 0.00 0.00 0.00 2.77
2419 2555 0.981183 TGCTATGGGGACGACAAAGT 59.019 50.000 0.00 0.00 0.00 2.66
2420 2556 1.349688 TGCTATGGGGACGACAAAGTT 59.650 47.619 0.00 0.00 0.00 2.66
2421 2557 2.224670 TGCTATGGGGACGACAAAGTTT 60.225 45.455 0.00 0.00 0.00 2.66
2422 2558 2.161609 GCTATGGGGACGACAAAGTTTG 59.838 50.000 14.13 14.13 0.00 2.93
2423 2559 1.616159 ATGGGGACGACAAAGTTTGG 58.384 50.000 19.45 5.52 34.12 3.28
2424 2560 0.547075 TGGGGACGACAAAGTTTGGA 59.453 50.000 19.45 0.00 34.12 3.53
2425 2561 0.949397 GGGGACGACAAAGTTTGGAC 59.051 55.000 19.45 11.70 34.12 4.02
2426 2562 0.584876 GGGACGACAAAGTTTGGACG 59.415 55.000 24.75 24.75 39.24 4.79
2427 2563 1.574134 GGACGACAAAGTTTGGACGA 58.426 50.000 29.57 0.00 37.74 4.20
2428 2564 1.259770 GGACGACAAAGTTTGGACGAC 59.740 52.381 29.57 25.12 37.74 4.34
2429 2565 2.199236 GACGACAAAGTTTGGACGACT 58.801 47.619 29.57 16.78 37.74 4.18
2430 2566 2.199236 ACGACAAAGTTTGGACGACTC 58.801 47.619 29.57 14.67 37.74 3.36
2431 2567 2.198406 CGACAAAGTTTGGACGACTCA 58.802 47.619 23.24 0.00 36.97 3.41
2432 2568 2.800544 CGACAAAGTTTGGACGACTCAT 59.199 45.455 23.24 1.40 36.97 2.90
2433 2569 3.362986 CGACAAAGTTTGGACGACTCATG 60.363 47.826 23.24 0.00 36.97 3.07
2434 2570 3.804036 ACAAAGTTTGGACGACTCATGA 58.196 40.909 19.45 0.00 34.12 3.07
2435 2571 4.196193 ACAAAGTTTGGACGACTCATGAA 58.804 39.130 19.45 0.00 34.12 2.57
2436 2572 4.035208 ACAAAGTTTGGACGACTCATGAAC 59.965 41.667 19.45 0.00 34.12 3.18
2437 2573 2.404215 AGTTTGGACGACTCATGAACG 58.596 47.619 16.73 16.73 0.00 3.95
2438 2574 2.035449 AGTTTGGACGACTCATGAACGA 59.965 45.455 22.60 4.10 0.00 3.85
2439 2575 2.060326 TTGGACGACTCATGAACGAC 57.940 50.000 22.60 17.58 0.00 4.34
2440 2576 0.109919 TGGACGACTCATGAACGACG 60.110 55.000 22.60 14.59 0.00 5.12
2441 2577 0.167470 GGACGACTCATGAACGACGA 59.833 55.000 22.60 0.00 0.00 4.20
2442 2578 1.202154 GGACGACTCATGAACGACGAT 60.202 52.381 22.60 5.94 0.00 3.73
2443 2579 2.516923 GACGACTCATGAACGACGATT 58.483 47.619 22.60 5.64 0.00 3.34
2444 2580 3.486375 GGACGACTCATGAACGACGATTA 60.486 47.826 22.60 0.00 0.00 1.75
2445 2581 4.087510 ACGACTCATGAACGACGATTAA 57.912 40.909 22.60 0.00 0.00 1.40
2446 2582 4.478699 ACGACTCATGAACGACGATTAAA 58.521 39.130 22.60 0.00 0.00 1.52
2447 2583 5.100259 ACGACTCATGAACGACGATTAAAT 58.900 37.500 22.60 1.21 0.00 1.40
2448 2584 5.229469 ACGACTCATGAACGACGATTAAATC 59.771 40.000 22.60 0.00 0.00 2.17
2461 2597 4.295133 GATTAAATCGAGCCGACGAATC 57.705 45.455 0.00 6.02 45.16 2.52
2462 2598 3.431922 TTAAATCGAGCCGACGAATCT 57.568 42.857 0.00 0.00 45.16 2.40
2463 2599 1.841450 AAATCGAGCCGACGAATCTC 58.159 50.000 0.00 0.00 45.16 2.75
2464 2600 0.738975 AATCGAGCCGACGAATCTCA 59.261 50.000 0.00 0.00 45.16 3.27
2465 2601 0.738975 ATCGAGCCGACGAATCTCAA 59.261 50.000 0.00 0.00 45.16 3.02
2466 2602 0.098905 TCGAGCCGACGAATCTCAAG 59.901 55.000 0.00 0.00 39.34 3.02
2467 2603 1.475441 CGAGCCGACGAATCTCAAGC 61.475 60.000 0.00 0.00 35.09 4.01
2468 2604 0.458543 GAGCCGACGAATCTCAAGCA 60.459 55.000 0.00 0.00 0.00 3.91
2469 2605 0.737715 AGCCGACGAATCTCAAGCAC 60.738 55.000 0.00 0.00 0.00 4.40
2470 2606 1.014044 GCCGACGAATCTCAAGCACA 61.014 55.000 0.00 0.00 0.00 4.57
2471 2607 0.994995 CCGACGAATCTCAAGCACAG 59.005 55.000 0.00 0.00 0.00 3.66
2472 2608 0.368227 CGACGAATCTCAAGCACAGC 59.632 55.000 0.00 0.00 0.00 4.40
2473 2609 1.719600 GACGAATCTCAAGCACAGCT 58.280 50.000 0.00 0.00 42.56 4.24
2474 2610 1.392853 GACGAATCTCAAGCACAGCTG 59.607 52.381 13.48 13.48 39.62 4.24
2475 2611 1.001293 ACGAATCTCAAGCACAGCTGA 59.999 47.619 23.35 0.00 39.62 4.26
2476 2612 1.659601 CGAATCTCAAGCACAGCTGAG 59.340 52.381 23.35 14.77 39.62 3.35
2477 2613 1.397692 GAATCTCAAGCACAGCTGAGC 59.602 52.381 26.32 26.32 39.62 4.26
2478 2614 0.323957 ATCTCAAGCACAGCTGAGCA 59.676 50.000 32.94 15.97 39.62 4.26
2479 2615 0.320508 TCTCAAGCACAGCTGAGCAG 60.321 55.000 32.94 25.03 39.62 4.24
2480 2616 0.603172 CTCAAGCACAGCTGAGCAGT 60.603 55.000 32.94 20.04 39.62 4.40
2481 2617 0.883370 TCAAGCACAGCTGAGCAGTG 60.883 55.000 32.94 28.15 46.31 3.66
2482 2618 1.600076 AAGCACAGCTGAGCAGTGG 60.600 57.895 32.94 12.25 44.30 4.00
2483 2619 3.735029 GCACAGCTGAGCAGTGGC 61.735 66.667 28.20 17.34 44.30 5.01
2484 2620 3.054503 CACAGCTGAGCAGTGGCC 61.055 66.667 23.35 0.00 41.28 5.36
2485 2621 4.694233 ACAGCTGAGCAGTGGCCG 62.694 66.667 23.35 0.00 42.56 6.13
2491 2627 4.479993 GAGCAGTGGCCGCTGGAT 62.480 66.667 39.76 23.81 40.63 3.41
2492 2628 4.479993 AGCAGTGGCCGCTGGATC 62.480 66.667 39.76 26.53 42.56 3.36
2494 2630 3.790437 CAGTGGCCGCTGGATCCT 61.790 66.667 34.42 1.79 33.11 3.24
2495 2631 3.011517 AGTGGCCGCTGGATCCTT 61.012 61.111 20.48 0.00 0.00 3.36
2496 2632 2.044946 GTGGCCGCTGGATCCTTT 60.045 61.111 14.23 0.00 0.00 3.11
2497 2633 2.045045 TGGCCGCTGGATCCTTTG 60.045 61.111 14.23 4.50 0.00 2.77
2498 2634 2.830370 GGCCGCTGGATCCTTTGG 60.830 66.667 14.23 12.39 0.00 3.28
2499 2635 2.044946 GCCGCTGGATCCTTTGGT 60.045 61.111 14.23 0.00 0.00 3.67
2500 2636 2.115291 GCCGCTGGATCCTTTGGTC 61.115 63.158 14.23 4.69 0.00 4.02
2501 2637 1.815421 CCGCTGGATCCTTTGGTCG 60.815 63.158 14.23 7.04 0.00 4.79
2502 2638 1.079127 CGCTGGATCCTTTGGTCGT 60.079 57.895 14.23 0.00 0.00 4.34
2503 2639 1.361668 CGCTGGATCCTTTGGTCGTG 61.362 60.000 14.23 0.00 0.00 4.35
2504 2640 1.648467 GCTGGATCCTTTGGTCGTGC 61.648 60.000 14.23 0.12 0.00 5.34
2505 2641 0.321564 CTGGATCCTTTGGTCGTGCA 60.322 55.000 14.23 0.00 0.00 4.57
2506 2642 0.605319 TGGATCCTTTGGTCGTGCAC 60.605 55.000 14.23 6.82 0.00 4.57
2507 2643 0.321653 GGATCCTTTGGTCGTGCACT 60.322 55.000 16.19 0.00 0.00 4.40
2508 2644 1.523758 GATCCTTTGGTCGTGCACTT 58.476 50.000 16.19 0.00 0.00 3.16
2509 2645 2.614481 GGATCCTTTGGTCGTGCACTTA 60.614 50.000 16.19 0.00 0.00 2.24
2510 2646 2.851263 TCCTTTGGTCGTGCACTTAT 57.149 45.000 16.19 0.00 0.00 1.73
2511 2647 2.695359 TCCTTTGGTCGTGCACTTATC 58.305 47.619 16.19 3.73 0.00 1.75
2512 2648 1.393539 CCTTTGGTCGTGCACTTATCG 59.606 52.381 16.19 0.55 0.00 2.92
2513 2649 2.066262 CTTTGGTCGTGCACTTATCGT 58.934 47.619 16.19 0.00 0.00 3.73
2514 2650 1.705256 TTGGTCGTGCACTTATCGTC 58.295 50.000 16.19 0.00 0.00 4.20
2515 2651 0.108992 TGGTCGTGCACTTATCGTCC 60.109 55.000 16.19 9.01 34.53 4.79
2516 2652 0.172803 GGTCGTGCACTTATCGTCCT 59.827 55.000 16.19 0.00 32.18 3.85
2517 2653 1.546834 GTCGTGCACTTATCGTCCTC 58.453 55.000 16.19 0.00 0.00 3.71
2518 2654 1.135489 GTCGTGCACTTATCGTCCTCA 60.135 52.381 16.19 0.00 0.00 3.86
2519 2655 1.135489 TCGTGCACTTATCGTCCTCAC 60.135 52.381 16.19 0.00 0.00 3.51
2520 2656 1.402325 CGTGCACTTATCGTCCTCACA 60.402 52.381 16.19 0.00 0.00 3.58
2521 2657 1.993370 GTGCACTTATCGTCCTCACAC 59.007 52.381 10.32 0.00 0.00 3.82
2522 2658 1.893137 TGCACTTATCGTCCTCACACT 59.107 47.619 0.00 0.00 0.00 3.55
2523 2659 2.263077 GCACTTATCGTCCTCACACTG 58.737 52.381 0.00 0.00 0.00 3.66
2524 2660 2.352814 GCACTTATCGTCCTCACACTGT 60.353 50.000 0.00 0.00 0.00 3.55
2525 2661 3.502920 CACTTATCGTCCTCACACTGTC 58.497 50.000 0.00 0.00 0.00 3.51
2526 2662 2.161808 ACTTATCGTCCTCACACTGTCG 59.838 50.000 0.00 0.00 0.00 4.35
2527 2663 1.817357 TATCGTCCTCACACTGTCGT 58.183 50.000 0.00 0.00 0.00 4.34
2528 2664 0.241213 ATCGTCCTCACACTGTCGTG 59.759 55.000 4.63 4.63 46.63 4.35
2537 2673 3.812577 CACTGTCGTGTATGGAGCA 57.187 52.632 0.00 0.00 36.39 4.26
2538 2674 1.633561 CACTGTCGTGTATGGAGCAG 58.366 55.000 0.00 0.00 36.39 4.24
2539 2675 1.067565 CACTGTCGTGTATGGAGCAGT 60.068 52.381 0.00 0.00 37.63 4.40
2540 2676 1.618837 ACTGTCGTGTATGGAGCAGTT 59.381 47.619 0.00 0.00 34.02 3.16
2541 2677 2.037251 ACTGTCGTGTATGGAGCAGTTT 59.963 45.455 0.00 0.00 34.02 2.66
2542 2678 2.668457 CTGTCGTGTATGGAGCAGTTTC 59.332 50.000 0.00 0.00 0.00 2.78
2543 2679 1.654105 GTCGTGTATGGAGCAGTTTCG 59.346 52.381 0.00 0.00 0.00 3.46
2544 2680 0.370273 CGTGTATGGAGCAGTTTCGC 59.630 55.000 0.00 0.00 0.00 4.70
2546 2682 2.076863 GTGTATGGAGCAGTTTCGCTT 58.923 47.619 0.00 0.00 44.01 4.68
2547 2683 2.094417 GTGTATGGAGCAGTTTCGCTTC 59.906 50.000 0.00 0.00 44.01 3.86
2549 2685 2.918571 TGGAGCAGTTTCGCTTCAG 58.081 52.632 0.00 0.00 42.76 3.02
2638 2779 5.107989 GGATCACTACGTTATTACATGTGCG 60.108 44.000 9.11 7.70 0.00 5.34
2651 2792 3.997762 ACATGTGCGTAAAGTGTCCTTA 58.002 40.909 0.00 0.00 0.00 2.69
2652 2793 3.994392 ACATGTGCGTAAAGTGTCCTTAG 59.006 43.478 0.00 0.00 0.00 2.18
2653 2794 3.738830 TGTGCGTAAAGTGTCCTTAGT 57.261 42.857 0.00 0.00 0.00 2.24
2654 2795 3.645884 TGTGCGTAAAGTGTCCTTAGTC 58.354 45.455 0.00 0.00 0.00 2.59
2655 2796 2.660236 GTGCGTAAAGTGTCCTTAGTCG 59.340 50.000 0.00 0.00 0.00 4.18
2661 2802 5.392811 CGTAAAGTGTCCTTAGTCGGAGAAT 60.393 44.000 0.00 0.00 39.69 2.40
2676 2817 3.384789 CGGAGAATCAATGTACTCCCTCA 59.615 47.826 0.00 0.00 43.98 3.86
2677 2818 4.698575 GGAGAATCAATGTACTCCCTCAC 58.301 47.826 0.00 0.00 41.89 3.51
2680 2821 5.276440 AGAATCAATGTACTCCCTCACTCT 58.724 41.667 0.00 0.00 0.00 3.24
2691 2832 6.723298 ACTCCCTCACTCTATGAATAAGTG 57.277 41.667 0.00 0.00 41.38 3.16
2692 2833 6.198639 ACTCCCTCACTCTATGAATAAGTGT 58.801 40.000 0.00 0.00 40.94 3.55
2693 2834 7.355101 ACTCCCTCACTCTATGAATAAGTGTA 58.645 38.462 0.00 0.00 40.94 2.90
2694 2835 7.285858 ACTCCCTCACTCTATGAATAAGTGTAC 59.714 40.741 0.00 0.00 40.94 2.90
2695 2836 7.355101 TCCCTCACTCTATGAATAAGTGTACT 58.645 38.462 0.00 0.00 40.94 2.73
2697 2838 8.138712 CCCTCACTCTATGAATAAGTGTACTTC 58.861 40.741 0.00 0.00 40.94 3.01
2699 2840 8.589701 TCACTCTATGAATAAGTGTACTTCCA 57.410 34.615 0.00 0.00 40.94 3.53
2700 2841 8.467598 TCACTCTATGAATAAGTGTACTTCCAC 58.532 37.037 0.00 0.00 40.94 4.02
2701 2842 7.707035 CACTCTATGAATAAGTGTACTTCCACC 59.293 40.741 0.00 0.00 36.50 4.61
2842 2983 9.613428 TGATACTAATTTAGTGCCATATATGCC 57.387 33.333 17.47 0.00 39.81 4.40
2858 2999 2.585263 GCCGCATGCAGCAATTTAG 58.415 52.632 20.90 0.00 46.13 1.85
2874 3015 5.455392 CAATTTAGTGCACCTGAAACTCTG 58.545 41.667 14.63 6.88 0.00 3.35
2888 3029 5.245531 TGAAACTCTGAATATGTGACCACC 58.754 41.667 0.00 0.00 0.00 4.61
2963 3104 1.741706 AGCGATTTGATGCACCTGAAG 59.258 47.619 0.00 0.00 0.00 3.02
2966 3107 2.223203 CGATTTGATGCACCTGAAGCTC 60.223 50.000 0.00 0.00 0.00 4.09
2983 3124 4.620589 AGCTCTGAATATGTGATGGAGG 57.379 45.455 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 2.830370 GCCATGCACACTAGGGCC 60.830 66.667 0.00 0.00 38.70 5.80
165 181 6.262496 GGGAGGATTAATTAGTTTTTCTCCCG 59.738 42.308 16.23 0.00 45.44 5.14
175 191 9.355916 GCTTGATTTAAGGGAGGATTAATTAGT 57.644 33.333 0.00 0.00 36.87 2.24
176 192 8.797438 GGCTTGATTTAAGGGAGGATTAATTAG 58.203 37.037 0.00 0.00 36.87 1.73
177 193 8.285891 TGGCTTGATTTAAGGGAGGATTAATTA 58.714 33.333 0.00 0.00 36.87 1.40
180 196 6.086011 TGGCTTGATTTAAGGGAGGATTAA 57.914 37.500 0.00 0.00 36.87 1.40
191 207 6.723977 AGGTAGGTCATTTTGGCTTGATTTAA 59.276 34.615 0.00 0.00 0.00 1.52
306 328 8.688151 CAAGAAATGGAAGCTACTACTACTACT 58.312 37.037 0.00 0.00 0.00 2.57
307 329 8.859517 CAAGAAATGGAAGCTACTACTACTAC 57.140 38.462 0.00 0.00 0.00 2.73
365 420 2.124151 CCCCTTGGATTGAGCCGG 60.124 66.667 0.00 0.00 0.00 6.13
384 439 3.120321 ACTACTCCAAAACACGATGCA 57.880 42.857 0.00 0.00 0.00 3.96
393 448 3.778629 CCCTAGCCCTAACTACTCCAAAA 59.221 47.826 0.00 0.00 0.00 2.44
402 457 1.636769 GCAAGCCCCTAGCCCTAACT 61.637 60.000 0.00 0.00 45.47 2.24
491 552 2.041081 TCCGAGTCACATGGGGATTTTT 59.959 45.455 0.00 0.00 0.00 1.94
492 553 1.633432 TCCGAGTCACATGGGGATTTT 59.367 47.619 0.00 0.00 0.00 1.82
493 554 1.210478 CTCCGAGTCACATGGGGATTT 59.790 52.381 0.00 0.00 0.00 2.17
494 555 0.833287 CTCCGAGTCACATGGGGATT 59.167 55.000 0.00 0.00 0.00 3.01
495 556 1.690219 GCTCCGAGTCACATGGGGAT 61.690 60.000 0.00 0.00 0.00 3.85
496 557 2.359169 GCTCCGAGTCACATGGGGA 61.359 63.158 0.00 0.00 0.00 4.81
497 558 2.187946 GCTCCGAGTCACATGGGG 59.812 66.667 0.00 0.00 0.00 4.96
498 559 2.202797 CGCTCCGAGTCACATGGG 60.203 66.667 0.00 0.00 0.00 4.00
499 560 2.202797 CCGCTCCGAGTCACATGG 60.203 66.667 0.00 0.00 0.00 3.66
500 561 2.887568 GCCGCTCCGAGTCACATG 60.888 66.667 0.00 0.00 0.00 3.21
501 562 4.148825 GGCCGCTCCGAGTCACAT 62.149 66.667 0.00 0.00 0.00 3.21
563 624 7.823745 ACATTTTGATCAGAAGTAAACCAGT 57.176 32.000 4.85 0.00 0.00 4.00
589 650 2.476873 ACGTACGAGTGATGAGCATC 57.523 50.000 24.41 3.55 38.29 3.91
626 702 5.288712 CGTACGACTAAACAATCATCAGCTT 59.711 40.000 10.44 0.00 0.00 3.74
642 718 3.444742 TGGGATCAACATTACGTACGACT 59.555 43.478 24.41 2.35 0.00 4.18
643 719 3.772932 TGGGATCAACATTACGTACGAC 58.227 45.455 24.41 0.13 0.00 4.34
645 721 5.292345 TCATTTGGGATCAACATTACGTACG 59.708 40.000 15.01 15.01 31.78 3.67
646 722 6.671614 TCATTTGGGATCAACATTACGTAC 57.328 37.500 0.00 0.00 31.78 3.67
648 724 6.773976 AATCATTTGGGATCAACATTACGT 57.226 33.333 0.00 0.00 31.78 3.57
649 725 8.620416 TCTTAATCATTTGGGATCAACATTACG 58.380 33.333 0.00 0.00 31.78 3.18
650 726 9.736023 GTCTTAATCATTTGGGATCAACATTAC 57.264 33.333 0.00 0.00 31.78 1.89
682 769 1.480212 TTCCACTGATCCGTGCCAGT 61.480 55.000 11.47 0.00 43.73 4.00
683 770 1.021390 GTTCCACTGATCCGTGCCAG 61.021 60.000 11.47 0.00 36.53 4.85
684 771 1.003839 GTTCCACTGATCCGTGCCA 60.004 57.895 11.47 0.00 33.60 4.92
752 839 2.690778 GCCGACTCTGCCGCATTTT 61.691 57.895 0.00 0.00 0.00 1.82
786 873 0.712380 ATTCCCCATTTCCACTGGCT 59.288 50.000 0.00 0.00 32.08 4.75
792 879 1.919654 TCGAAGGATTCCCCATTTCCA 59.080 47.619 0.00 0.00 43.81 3.53
793 880 2.729028 TCGAAGGATTCCCCATTTCC 57.271 50.000 0.00 0.00 43.81 3.13
794 881 4.674362 CGTTTTCGAAGGATTCCCCATTTC 60.674 45.833 0.00 0.00 43.81 2.17
795 882 3.192633 CGTTTTCGAAGGATTCCCCATTT 59.807 43.478 0.00 0.00 43.81 2.32
796 883 2.752903 CGTTTTCGAAGGATTCCCCATT 59.247 45.455 0.00 0.00 43.81 3.16
797 884 2.290705 ACGTTTTCGAAGGATTCCCCAT 60.291 45.455 0.00 0.00 43.81 4.00
798 885 1.072648 ACGTTTTCGAAGGATTCCCCA 59.927 47.619 0.00 0.00 43.81 4.96
799 886 1.817357 ACGTTTTCGAAGGATTCCCC 58.183 50.000 0.00 0.00 43.81 4.81
863 960 1.026182 TGCCATGCACGATTCCTGAC 61.026 55.000 0.00 0.00 31.71 3.51
1188 1306 2.580815 CTCATCCAGTCGGCAGCA 59.419 61.111 0.00 0.00 0.00 4.41
1212 1330 2.183555 CCTCCGTAGAACGTGGCC 59.816 66.667 0.00 0.00 40.58 5.36
1218 1336 0.458025 CGTTGCTCCCTCCGTAGAAC 60.458 60.000 0.00 0.00 0.00 3.01
1262 1380 2.887568 GGAGCGCAGTCGTGGATG 60.888 66.667 11.47 0.00 38.14 3.51
1286 1404 2.489329 AGAAGTGCAATGCAAATACGCT 59.511 40.909 10.44 0.00 41.47 5.07
1306 1424 3.705638 CATATCCACGGCGCGCAG 61.706 66.667 34.42 31.83 0.00 5.18
1337 1457 1.302383 TGCCATTAGTTCCAACGCCG 61.302 55.000 0.00 0.00 0.00 6.46
1345 1465 2.823829 CGCCGCCTGCCATTAGTTC 61.824 63.158 0.00 0.00 36.24 3.01
1774 1901 2.512515 GATCTGCACCGCCCTGAC 60.513 66.667 0.00 0.00 0.00 3.51
2034 2161 0.949397 AAACGGAAAGGAAAGGCGAC 59.051 50.000 0.00 0.00 0.00 5.19
2037 2164 1.400629 GCGTAAACGGAAAGGAAAGGC 60.401 52.381 4.49 0.00 40.23 4.35
2039 2166 2.148768 AGGCGTAAACGGAAAGGAAAG 58.851 47.619 4.49 0.00 40.23 2.62
2040 2167 2.259266 AGGCGTAAACGGAAAGGAAA 57.741 45.000 4.49 0.00 40.23 3.13
2044 2174 2.221517 TCGAAAAGGCGTAAACGGAAAG 59.778 45.455 4.49 0.00 40.23 2.62
2058 2188 3.832276 TCCCAAATGCGAAATCGAAAAG 58.168 40.909 7.06 0.00 43.02 2.27
2081 2211 8.268850 TGAGAATGAGGCAAATCTTACTTAAC 57.731 34.615 0.00 0.00 0.00 2.01
2094 2224 1.144298 CCCATCCATGAGAATGAGGCA 59.856 52.381 0.00 0.00 0.00 4.75
2154 2284 1.973281 ACCTCAGCCATGCAAACCG 60.973 57.895 0.00 0.00 0.00 4.44
2210 2340 3.869272 CAGCCGGTCATCGCAAGC 61.869 66.667 1.90 0.00 37.59 4.01
2353 2489 3.548668 CGCACATGCATTCATTTAACTGG 59.451 43.478 0.00 0.00 42.21 4.00
2354 2490 4.030865 CACGCACATGCATTCATTTAACTG 59.969 41.667 0.00 0.00 42.21 3.16
2355 2491 4.082841 TCACGCACATGCATTCATTTAACT 60.083 37.500 0.00 0.00 42.21 2.24
2391 2527 2.225467 GTCCCCATAGCATTGCTCTTC 58.775 52.381 15.81 0.00 40.44 2.87
2392 2528 1.475751 CGTCCCCATAGCATTGCTCTT 60.476 52.381 15.81 0.94 40.44 2.85
2394 2530 0.106708 TCGTCCCCATAGCATTGCTC 59.893 55.000 15.81 0.00 40.44 4.26
2395 2531 0.179045 GTCGTCCCCATAGCATTGCT 60.179 55.000 16.63 16.63 43.41 3.91
2396 2532 0.463654 TGTCGTCCCCATAGCATTGC 60.464 55.000 0.00 0.00 0.00 3.56
2397 2533 2.036958 TTGTCGTCCCCATAGCATTG 57.963 50.000 0.00 0.00 0.00 2.82
2398 2534 2.026262 ACTTTGTCGTCCCCATAGCATT 60.026 45.455 0.00 0.00 0.00 3.56
2399 2535 1.559682 ACTTTGTCGTCCCCATAGCAT 59.440 47.619 0.00 0.00 0.00 3.79
2400 2536 0.981183 ACTTTGTCGTCCCCATAGCA 59.019 50.000 0.00 0.00 0.00 3.49
2401 2537 2.109425 AACTTTGTCGTCCCCATAGC 57.891 50.000 0.00 0.00 0.00 2.97
2402 2538 2.747446 CCAAACTTTGTCGTCCCCATAG 59.253 50.000 0.88 0.00 0.00 2.23
2403 2539 2.372504 TCCAAACTTTGTCGTCCCCATA 59.627 45.455 0.88 0.00 0.00 2.74
2404 2540 1.144093 TCCAAACTTTGTCGTCCCCAT 59.856 47.619 0.88 0.00 0.00 4.00
2405 2541 0.547075 TCCAAACTTTGTCGTCCCCA 59.453 50.000 0.88 0.00 0.00 4.96
2406 2542 0.949397 GTCCAAACTTTGTCGTCCCC 59.051 55.000 0.88 0.00 0.00 4.81
2407 2543 0.584876 CGTCCAAACTTTGTCGTCCC 59.415 55.000 0.88 0.00 0.00 4.46
2408 2544 1.259770 GTCGTCCAAACTTTGTCGTCC 59.740 52.381 12.66 5.41 0.00 4.79
2409 2545 2.199236 AGTCGTCCAAACTTTGTCGTC 58.801 47.619 12.66 9.26 0.00 4.20
2410 2546 2.199236 GAGTCGTCCAAACTTTGTCGT 58.801 47.619 12.66 0.58 0.00 4.34
2411 2547 2.198406 TGAGTCGTCCAAACTTTGTCG 58.802 47.619 0.88 5.63 0.00 4.35
2412 2548 3.807622 TCATGAGTCGTCCAAACTTTGTC 59.192 43.478 0.00 0.00 0.00 3.18
2413 2549 3.804036 TCATGAGTCGTCCAAACTTTGT 58.196 40.909 0.00 0.00 0.00 2.83
2414 2550 4.527564 GTTCATGAGTCGTCCAAACTTTG 58.472 43.478 0.00 0.00 0.00 2.77
2415 2551 3.247648 CGTTCATGAGTCGTCCAAACTTT 59.752 43.478 12.20 0.00 0.00 2.66
2416 2552 2.800544 CGTTCATGAGTCGTCCAAACTT 59.199 45.455 12.20 0.00 0.00 2.66
2417 2553 2.035449 TCGTTCATGAGTCGTCCAAACT 59.965 45.455 17.39 0.00 0.00 2.66
2418 2554 2.155155 GTCGTTCATGAGTCGTCCAAAC 59.845 50.000 17.39 8.13 0.00 2.93
2419 2555 2.400399 GTCGTTCATGAGTCGTCCAAA 58.600 47.619 17.39 1.26 0.00 3.28
2420 2556 1.664874 CGTCGTTCATGAGTCGTCCAA 60.665 52.381 17.39 1.55 0.00 3.53
2421 2557 0.109919 CGTCGTTCATGAGTCGTCCA 60.110 55.000 17.39 1.83 0.00 4.02
2422 2558 0.167470 TCGTCGTTCATGAGTCGTCC 59.833 55.000 17.39 10.99 0.00 4.79
2423 2559 2.175530 ATCGTCGTTCATGAGTCGTC 57.824 50.000 17.39 12.91 0.00 4.20
2424 2560 2.631418 AATCGTCGTTCATGAGTCGT 57.369 45.000 17.39 1.55 0.00 4.34
2425 2561 5.621635 ATTTAATCGTCGTTCATGAGTCG 57.378 39.130 13.64 13.64 0.00 4.18
2440 2576 3.982058 AGATTCGTCGGCTCGATTTAATC 59.018 43.478 14.38 14.38 38.42 1.75
2441 2577 3.978687 AGATTCGTCGGCTCGATTTAAT 58.021 40.909 0.67 2.40 38.42 1.40
2442 2578 3.181494 TGAGATTCGTCGGCTCGATTTAA 60.181 43.478 0.67 0.00 38.42 1.52
2443 2579 2.356695 TGAGATTCGTCGGCTCGATTTA 59.643 45.455 0.67 0.00 38.42 1.40
2444 2580 1.134367 TGAGATTCGTCGGCTCGATTT 59.866 47.619 0.67 0.00 38.42 2.17
2445 2581 0.738975 TGAGATTCGTCGGCTCGATT 59.261 50.000 0.67 0.41 38.42 3.34
2446 2582 0.738975 TTGAGATTCGTCGGCTCGAT 59.261 50.000 0.67 0.00 38.42 3.59
2447 2583 0.098905 CTTGAGATTCGTCGGCTCGA 59.901 55.000 0.00 0.00 38.08 4.04
2448 2584 1.475441 GCTTGAGATTCGTCGGCTCG 61.475 60.000 0.00 0.00 0.00 5.03
2449 2585 0.458543 TGCTTGAGATTCGTCGGCTC 60.459 55.000 0.00 0.00 0.00 4.70
2450 2586 0.737715 GTGCTTGAGATTCGTCGGCT 60.738 55.000 0.00 0.00 0.00 5.52
2451 2587 1.014044 TGTGCTTGAGATTCGTCGGC 61.014 55.000 0.00 0.00 0.00 5.54
2452 2588 0.994995 CTGTGCTTGAGATTCGTCGG 59.005 55.000 0.00 0.00 0.00 4.79
2453 2589 0.368227 GCTGTGCTTGAGATTCGTCG 59.632 55.000 0.00 0.00 0.00 5.12
2454 2590 1.392853 CAGCTGTGCTTGAGATTCGTC 59.607 52.381 5.25 0.00 36.40 4.20
2455 2591 1.001293 TCAGCTGTGCTTGAGATTCGT 59.999 47.619 14.67 0.00 36.40 3.85
2456 2592 1.659601 CTCAGCTGTGCTTGAGATTCG 59.340 52.381 14.67 0.00 36.40 3.34
2457 2593 1.397692 GCTCAGCTGTGCTTGAGATTC 59.602 52.381 28.75 1.53 36.40 2.52
2458 2594 1.271217 TGCTCAGCTGTGCTTGAGATT 60.271 47.619 33.41 0.00 36.40 2.40
2459 2595 0.323957 TGCTCAGCTGTGCTTGAGAT 59.676 50.000 33.41 0.00 36.40 2.75
2460 2596 0.320508 CTGCTCAGCTGTGCTTGAGA 60.321 55.000 33.41 17.23 36.40 3.27
2461 2597 0.603172 ACTGCTCAGCTGTGCTTGAG 60.603 55.000 33.41 26.08 39.15 3.02
2462 2598 1.448924 ACTGCTCAGCTGTGCTTGA 59.551 52.632 33.41 17.87 39.15 3.02
2463 2599 4.060372 ACTGCTCAGCTGTGCTTG 57.940 55.556 33.41 27.57 39.15 4.01
2468 2604 4.694233 CGGCCACTGCTCAGCTGT 62.694 66.667 14.67 2.78 41.16 4.40
2474 2610 4.479993 ATCCAGCGGCCACTGCTC 62.480 66.667 15.67 0.00 41.72 4.26
2475 2611 4.479993 GATCCAGCGGCCACTGCT 62.480 66.667 15.67 6.52 45.31 4.24
2477 2613 2.826777 AAAGGATCCAGCGGCCACTG 62.827 60.000 15.82 14.15 37.42 3.66
2478 2614 2.606587 AAAGGATCCAGCGGCCACT 61.607 57.895 15.82 0.00 0.00 4.00
2479 2615 2.044946 AAAGGATCCAGCGGCCAC 60.045 61.111 15.82 0.00 0.00 5.01
2480 2616 2.045045 CAAAGGATCCAGCGGCCA 60.045 61.111 15.82 0.00 0.00 5.36
2481 2617 2.830370 CCAAAGGATCCAGCGGCC 60.830 66.667 15.82 0.00 0.00 6.13
2482 2618 2.044946 ACCAAAGGATCCAGCGGC 60.045 61.111 15.82 0.00 0.00 6.53
2483 2619 1.815421 CGACCAAAGGATCCAGCGG 60.815 63.158 15.82 12.91 0.00 5.52
2484 2620 1.079127 ACGACCAAAGGATCCAGCG 60.079 57.895 15.82 10.05 0.00 5.18
2485 2621 1.648467 GCACGACCAAAGGATCCAGC 61.648 60.000 15.82 0.00 0.00 4.85
2486 2622 0.321564 TGCACGACCAAAGGATCCAG 60.322 55.000 15.82 3.03 0.00 3.86
2487 2623 0.605319 GTGCACGACCAAAGGATCCA 60.605 55.000 15.82 0.00 0.00 3.41
2488 2624 0.321653 AGTGCACGACCAAAGGATCC 60.322 55.000 12.01 2.48 0.00 3.36
2489 2625 1.523758 AAGTGCACGACCAAAGGATC 58.476 50.000 12.01 0.00 0.00 3.36
2490 2626 2.851263 TAAGTGCACGACCAAAGGAT 57.149 45.000 12.01 0.00 0.00 3.24
2491 2627 2.695359 GATAAGTGCACGACCAAAGGA 58.305 47.619 12.01 0.00 0.00 3.36
2492 2628 1.393539 CGATAAGTGCACGACCAAAGG 59.606 52.381 12.01 0.00 0.00 3.11
2493 2629 2.066262 ACGATAAGTGCACGACCAAAG 58.934 47.619 12.01 3.85 0.00 2.77
2494 2630 2.063266 GACGATAAGTGCACGACCAAA 58.937 47.619 12.01 0.00 0.00 3.28
2495 2631 1.670674 GGACGATAAGTGCACGACCAA 60.671 52.381 12.01 0.00 41.21 3.67
2496 2632 0.108992 GGACGATAAGTGCACGACCA 60.109 55.000 12.01 0.00 41.21 4.02
2497 2633 0.172803 AGGACGATAAGTGCACGACC 59.827 55.000 12.01 9.08 44.28 4.79
2498 2634 1.135489 TGAGGACGATAAGTGCACGAC 60.135 52.381 12.01 0.00 44.28 4.34
2499 2635 1.135489 GTGAGGACGATAAGTGCACGA 60.135 52.381 12.01 3.80 44.28 4.35
2500 2636 1.269166 GTGAGGACGATAAGTGCACG 58.731 55.000 12.01 0.95 44.28 5.34
2501 2637 1.993370 GTGTGAGGACGATAAGTGCAC 59.007 52.381 9.40 9.40 44.28 4.57
2502 2638 1.893137 AGTGTGAGGACGATAAGTGCA 59.107 47.619 0.00 0.00 44.28 4.57
2503 2639 2.263077 CAGTGTGAGGACGATAAGTGC 58.737 52.381 0.00 0.00 41.95 4.40
2504 2640 3.502920 GACAGTGTGAGGACGATAAGTG 58.497 50.000 0.00 0.00 0.00 3.16
2505 2641 2.161808 CGACAGTGTGAGGACGATAAGT 59.838 50.000 0.00 0.00 0.00 2.24
2506 2642 2.161808 ACGACAGTGTGAGGACGATAAG 59.838 50.000 0.00 0.00 0.00 1.73
2507 2643 2.095415 CACGACAGTGTGAGGACGATAA 60.095 50.000 0.00 0.00 42.55 1.75
2508 2644 1.467342 CACGACAGTGTGAGGACGATA 59.533 52.381 0.00 0.00 42.55 2.92
2509 2645 0.241213 CACGACAGTGTGAGGACGAT 59.759 55.000 0.00 0.00 42.55 3.73
2510 2646 1.652563 CACGACAGTGTGAGGACGA 59.347 57.895 0.00 0.00 42.55 4.20
2511 2647 4.228451 CACGACAGTGTGAGGACG 57.772 61.111 0.00 0.00 42.55 4.79
2520 2656 1.257743 ACTGCTCCATACACGACAGT 58.742 50.000 0.00 0.00 33.71 3.55
2521 2657 2.370281 AACTGCTCCATACACGACAG 57.630 50.000 0.00 0.00 0.00 3.51
2522 2658 2.683968 GAAACTGCTCCATACACGACA 58.316 47.619 0.00 0.00 0.00 4.35
2523 2659 1.654105 CGAAACTGCTCCATACACGAC 59.346 52.381 0.00 0.00 0.00 4.34
2524 2660 1.990799 CGAAACTGCTCCATACACGA 58.009 50.000 0.00 0.00 0.00 4.35
2525 2661 0.370273 GCGAAACTGCTCCATACACG 59.630 55.000 0.00 0.00 0.00 4.49
2526 2662 1.726853 AGCGAAACTGCTCCATACAC 58.273 50.000 0.00 0.00 42.95 2.90
2527 2663 2.289382 TGAAGCGAAACTGCTCCATACA 60.289 45.455 0.00 0.00 46.60 2.29
2528 2664 2.346803 TGAAGCGAAACTGCTCCATAC 58.653 47.619 0.00 0.00 46.60 2.39
2529 2665 2.621338 CTGAAGCGAAACTGCTCCATA 58.379 47.619 0.00 0.00 46.60 2.74
2530 2666 1.446907 CTGAAGCGAAACTGCTCCAT 58.553 50.000 0.00 0.00 46.60 3.41
2531 2667 0.603707 CCTGAAGCGAAACTGCTCCA 60.604 55.000 0.00 0.00 46.60 3.86
2532 2668 0.320771 TCCTGAAGCGAAACTGCTCC 60.321 55.000 0.00 0.00 46.60 4.70
2533 2669 1.512926 TTCCTGAAGCGAAACTGCTC 58.487 50.000 0.00 0.00 46.60 4.26
2535 2671 1.537202 ACATTCCTGAAGCGAAACTGC 59.463 47.619 0.00 0.00 0.00 4.40
2536 2672 2.666619 GCACATTCCTGAAGCGAAACTG 60.667 50.000 0.00 0.00 0.00 3.16
2537 2673 1.537202 GCACATTCCTGAAGCGAAACT 59.463 47.619 0.00 0.00 0.00 2.66
2538 2674 1.401539 GGCACATTCCTGAAGCGAAAC 60.402 52.381 0.00 0.00 0.00 2.78
2539 2675 0.881118 GGCACATTCCTGAAGCGAAA 59.119 50.000 0.00 0.00 0.00 3.46
2540 2676 0.960364 GGGCACATTCCTGAAGCGAA 60.960 55.000 0.00 0.00 0.00 4.70
2541 2677 1.377202 GGGCACATTCCTGAAGCGA 60.377 57.895 0.00 0.00 0.00 4.93
2542 2678 1.243342 TTGGGCACATTCCTGAAGCG 61.243 55.000 0.00 0.00 0.00 4.68
2543 2679 0.529378 CTTGGGCACATTCCTGAAGC 59.471 55.000 0.00 0.00 0.00 3.86
2544 2680 1.180029 CCTTGGGCACATTCCTGAAG 58.820 55.000 0.00 0.00 0.00 3.02
2545 2681 0.251742 CCCTTGGGCACATTCCTGAA 60.252 55.000 0.00 0.00 0.00 3.02
2546 2682 1.383799 CCCTTGGGCACATTCCTGA 59.616 57.895 0.00 0.00 0.00 3.86
2547 2683 0.331278 TACCCTTGGGCACATTCCTG 59.669 55.000 5.46 0.00 0.00 3.86
2548 2684 1.080638 TTACCCTTGGGCACATTCCT 58.919 50.000 5.46 0.00 0.00 3.36
2549 2685 1.931635 TTTACCCTTGGGCACATTCC 58.068 50.000 5.46 0.00 0.00 3.01
2638 2779 5.382618 TTCTCCGACTAAGGACACTTTAC 57.617 43.478 0.00 0.00 38.14 2.01
2651 2792 3.385111 GGGAGTACATTGATTCTCCGACT 59.615 47.826 14.78 0.00 45.04 4.18
2652 2793 3.385111 AGGGAGTACATTGATTCTCCGAC 59.615 47.826 14.78 7.18 45.04 4.79
2653 2794 3.637229 GAGGGAGTACATTGATTCTCCGA 59.363 47.826 14.78 0.00 45.04 4.55
2654 2795 3.384789 TGAGGGAGTACATTGATTCTCCG 59.615 47.826 14.78 0.00 45.04 4.63
2655 2796 4.407296 AGTGAGGGAGTACATTGATTCTCC 59.593 45.833 13.69 13.69 43.84 3.71
2661 2802 5.766590 TCATAGAGTGAGGGAGTACATTGA 58.233 41.667 0.00 0.00 31.80 2.57
2676 2817 7.147707 GGGTGGAAGTACACTTATTCATAGAGT 60.148 40.741 0.00 0.00 41.09 3.24
2677 2818 7.070074 AGGGTGGAAGTACACTTATTCATAGAG 59.930 40.741 0.00 0.00 41.09 2.43
2680 2821 7.504926 AAGGGTGGAAGTACACTTATTCATA 57.495 36.000 0.00 0.00 42.26 2.15
2842 2983 0.918619 GCACTAAATTGCTGCATGCG 59.081 50.000 14.09 9.16 46.63 4.73
2858 2999 4.697352 ACATATTCAGAGTTTCAGGTGCAC 59.303 41.667 8.80 8.80 0.00 4.57
2862 3003 5.013079 TGGTCACATATTCAGAGTTTCAGGT 59.987 40.000 0.00 0.00 0.00 4.00
2863 3004 5.352569 GTGGTCACATATTCAGAGTTTCAGG 59.647 44.000 0.00 0.00 0.00 3.86
2874 3015 9.482627 TTTTTGTTATTTGGTGGTCACATATTC 57.517 29.630 3.40 0.00 0.00 1.75
2904 3045 7.081526 AGAGAAAATTCATCACTGCATGTAC 57.918 36.000 0.00 0.00 0.00 2.90
2913 3054 6.529477 GCAAGGCTTAAGAGAAAATTCATCAC 59.471 38.462 6.67 0.00 0.00 3.06
2949 3090 1.348696 TCAGAGCTTCAGGTGCATCAA 59.651 47.619 0.00 0.00 0.00 2.57
2963 3104 3.672808 CCCTCCATCACATATTCAGAGC 58.327 50.000 0.00 0.00 0.00 4.09
2966 3107 3.784511 AGCCCTCCATCACATATTCAG 57.215 47.619 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.