Multiple sequence alignment - TraesCS5A01G171900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G171900 chr5A 100.000 5052 0 0 1 5052 365090236 365095287 0.000000e+00 9330
1 TraesCS5A01G171900 chr5B 95.642 1675 68 5 2427 4098 313958328 313960000 0.000000e+00 2684
2 TraesCS5A01G171900 chr5B 91.776 912 40 15 683 1577 313956868 313957761 0.000000e+00 1236
3 TraesCS5A01G171900 chr5B 85.470 819 50 18 4280 5046 313961824 313962625 0.000000e+00 789
4 TraesCS5A01G171900 chr5B 89.400 500 28 16 1834 2332 313957845 313958320 1.560000e-169 606
5 TraesCS5A01G171900 chr5B 85.080 563 76 6 2 563 42708297 42707742 7.340000e-158 568
6 TraesCS5A01G171900 chr5B 86.076 158 5 8 4088 4244 313961680 313961821 2.440000e-33 154
7 TraesCS5A01G171900 chr5B 95.294 85 4 0 2345 2429 228327987 228327903 8.820000e-28 135
8 TraesCS5A01G171900 chr5D 94.383 1620 50 16 745 2347 276706633 276708228 0.000000e+00 2449
9 TraesCS5A01G171900 chr5D 95.770 1371 43 2 2875 4244 276708579 276709935 0.000000e+00 2196
10 TraesCS5A01G171900 chr5D 86.692 804 50 28 4281 5046 276709939 276710723 0.000000e+00 839
11 TraesCS5A01G171900 chr5D 88.997 309 23 8 2427 2729 276708225 276708528 6.180000e-99 372
12 TraesCS5A01G171900 chr7D 86.655 562 72 3 2 563 573081302 573081860 2.000000e-173 619
13 TraesCS5A01G171900 chr6D 87.109 543 65 5 2 542 12176342 12176881 1.200000e-170 610
14 TraesCS5A01G171900 chr2A 87.269 542 60 9 2 542 739831626 739831093 1.200000e-170 610
15 TraesCS5A01G171900 chr3A 86.162 542 70 4 2 542 114574729 114574192 9.430000e-162 580
16 TraesCS5A01G171900 chr2D 85.902 532 67 7 2 531 528417284 528416759 1.230000e-155 560
17 TraesCS5A01G171900 chr2D 84.683 568 74 10 2 563 481651649 481651089 5.710000e-154 555
18 TraesCS5A01G171900 chr2D 81.277 689 113 14 2 680 96681879 96681197 1.240000e-150 544
19 TraesCS5A01G171900 chr2D 91.667 96 7 1 2345 2439 511922688 511922593 1.140000e-26 132
20 TraesCS5A01G171900 chr1B 82.500 640 92 16 2 632 426124397 426125025 1.240000e-150 544
21 TraesCS5A01G171900 chr1B 94.318 88 4 1 2345 2432 45483190 45483276 3.170000e-27 134
22 TraesCS5A01G171900 chr1B 94.318 88 4 1 2345 2432 45543560 45543646 3.170000e-27 134
23 TraesCS5A01G171900 chr1B 94.318 88 4 1 2345 2432 45600839 45600925 3.170000e-27 134
24 TraesCS5A01G171900 chr1B 94.318 88 4 1 2345 2432 45625535 45625621 3.170000e-27 134
25 TraesCS5A01G171900 chr7B 93.548 93 5 1 2341 2433 226902799 226902890 2.450000e-28 137
26 TraesCS5A01G171900 chrUn 90.385 104 8 2 2328 2429 94846953 94847056 8.820000e-28 135
27 TraesCS5A01G171900 chr3B 89.899 99 9 1 2345 2442 3660855 3660757 5.310000e-25 126


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 TraesCS5A01G171900 chr5A 365090236 365095287 5051 False 9330.0 9330 100.0000 1 5052 1 chr5A.!!$F1 5051
1 TraesCS5A01G171900 chr5B 313956868 313962625 5757 False 1093.8 2684 89.6728 683 5046 5 chr5B.!!$F1 4363
2 TraesCS5A01G171900 chr5B 42707742 42708297 555 True 568.0 568 85.0800 2 563 1 chr5B.!!$R1 561
3 TraesCS5A01G171900 chr5D 276706633 276710723 4090 False 1464.0 2449 91.4605 745 5046 4 chr5D.!!$F1 4301
4 TraesCS5A01G171900 chr7D 573081302 573081860 558 False 619.0 619 86.6550 2 563 1 chr7D.!!$F1 561
5 TraesCS5A01G171900 chr6D 12176342 12176881 539 False 610.0 610 87.1090 2 542 1 chr6D.!!$F1 540
6 TraesCS5A01G171900 chr2A 739831093 739831626 533 True 610.0 610 87.2690 2 542 1 chr2A.!!$R1 540
7 TraesCS5A01G171900 chr3A 114574192 114574729 537 True 580.0 580 86.1620 2 542 1 chr3A.!!$R1 540
8 TraesCS5A01G171900 chr2D 528416759 528417284 525 True 560.0 560 85.9020 2 531 1 chr2D.!!$R4 529
9 TraesCS5A01G171900 chr2D 481651089 481651649 560 True 555.0 555 84.6830 2 563 1 chr2D.!!$R2 561
10 TraesCS5A01G171900 chr2D 96681197 96681879 682 True 544.0 544 81.2770 2 680 1 chr2D.!!$R1 678
11 TraesCS5A01G171900 chr1B 426124397 426125025 628 False 544.0 544 82.5000 2 632 1 chr1B.!!$F5 630

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
856 889 0.321671 TCAACCTCACACTAGCCAGC 59.678 55.000 0.00 0.00 0.00 4.85 F
857 890 0.674895 CAACCTCACACTAGCCAGCC 60.675 60.000 0.00 0.00 0.00 4.85 F
1519 1564 1.131303 TGGAGAAATGGGGTCGTGGT 61.131 55.000 0.00 0.00 0.00 4.16 F
1674 1719 1.519898 CTGCAATTTGATGCCCGGC 60.520 57.895 1.04 1.04 45.83 6.13 F
2360 2425 0.042131 TTGTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00 F
3586 3666 0.461961 GACACTGGGGGATCTTCTCG 59.538 60.000 0.00 0.00 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2342 2407 0.928505 TATGGGACGGAGGGAGTACA 59.071 55.000 0.00 0.0 0.00 2.90 R
2345 2410 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.0 0.00 3.85 R
2346 2411 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.0 0.00 4.30 R
3595 3675 0.321830 TTAACGGGTACTTGGCCTGC 60.322 55.000 3.32 0.0 35.84 4.85 R
3865 3945 0.252148 TCAGCCCATGCCCATCAAAA 60.252 50.000 0.00 0.0 38.69 2.44 R
4746 6542 0.250252 TGCGCTCTTCATCACAACCA 60.250 50.000 9.73 0.0 0.00 3.67 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
89 90 3.632080 ACACGCATGTTCGGGGGA 61.632 61.111 0.08 0.00 34.46 4.81
97 98 4.547367 GTTCGGGGGAGCCGGATG 62.547 72.222 5.05 0.00 0.00 3.51
108 109 4.856801 CCGGATGGTCGGCCTTGG 62.857 72.222 7.97 0.00 43.71 3.61
207 209 3.754530 TCATTGCTCGTCGGCGGA 61.755 61.111 10.62 0.00 38.89 5.54
218 225 4.162690 CGGCGGAAAGAGGGAGGG 62.163 72.222 0.00 0.00 0.00 4.30
220 227 3.798511 GCGGAAAGAGGGAGGGGG 61.799 72.222 0.00 0.00 0.00 5.40
254 264 0.729816 GTGAGACGAGGCGAGTTGTC 60.730 60.000 0.00 0.00 0.00 3.18
274 284 2.589442 GGTTGTGGCGTTCACCGA 60.589 61.111 8.20 0.00 45.48 4.69
495 509 3.805307 CGTCTCGCTGACTCGGCT 61.805 66.667 8.25 0.00 43.25 5.52
497 511 2.359975 TCTCGCTGACTCGGCTGA 60.360 61.111 8.25 0.00 32.89 4.26
500 514 3.753434 CGCTGACTCGGCTGACCT 61.753 66.667 8.25 0.00 32.89 3.85
511 525 1.335132 GGCTGACCTATCCCCGTTCA 61.335 60.000 0.00 0.00 0.00 3.18
527 541 2.521996 GTTCACGTCAAAACCGCTTTT 58.478 42.857 0.00 0.00 0.00 2.27
563 580 0.691904 TATCGGGTTCGGTTTGGGTT 59.308 50.000 0.00 0.00 36.95 4.11
565 582 1.526455 CGGGTTCGGTTTGGGTTCA 60.526 57.895 0.00 0.00 0.00 3.18
581 598 3.460103 GGTTCACCAACACTAGTTTCGA 58.540 45.455 0.00 0.00 35.28 3.71
582 599 4.062991 GGTTCACCAACACTAGTTTCGAT 58.937 43.478 0.00 0.00 35.28 3.59
583 600 4.514066 GGTTCACCAACACTAGTTTCGATT 59.486 41.667 0.00 0.00 35.28 3.34
593 610 0.879090 AGTTTCGATTCAAACCGGCC 59.121 50.000 0.00 0.00 37.01 6.13
601 618 0.531200 TTCAAACCGGCCAAAAACGT 59.469 45.000 0.00 0.00 0.00 3.99
606 623 2.551912 CCGGCCAAAAACGTGCTCT 61.552 57.895 2.24 0.00 0.00 4.09
609 626 0.383949 GGCCAAAAACGTGCTCTTGA 59.616 50.000 0.00 0.00 0.00 3.02
611 628 2.535331 GCCAAAAACGTGCTCTTGAAA 58.465 42.857 0.00 0.00 0.00 2.69
622 639 2.294233 TGCTCTTGAAAACATGACTGGC 59.706 45.455 0.00 0.00 0.00 4.85
624 641 3.152341 CTCTTGAAAACATGACTGGCCT 58.848 45.455 3.32 0.00 0.00 5.19
625 642 4.326826 CTCTTGAAAACATGACTGGCCTA 58.673 43.478 3.32 0.00 0.00 3.93
627 644 5.324409 TCTTGAAAACATGACTGGCCTATT 58.676 37.500 3.32 0.00 0.00 1.73
718 740 0.537188 TCTTCCTGATCCAACGGCTC 59.463 55.000 0.00 0.00 0.00 4.70
723 745 1.202463 CCTGATCCAACGGCTCTGTAG 60.202 57.143 0.00 0.00 0.00 2.74
729 751 0.753262 CAACGGCTCTGTAGGCCTAT 59.247 55.000 17.38 0.00 46.73 2.57
735 757 2.483889 GGCTCTGTAGGCCTATGTCAAC 60.484 54.545 17.38 4.75 45.57 3.18
766 794 3.871594 GCTCGCACTATTTACCTGACAAT 59.128 43.478 0.00 0.00 0.00 2.71
797 825 2.239654 TGACCTATTTGCCCTTCTCTGG 59.760 50.000 0.00 0.00 0.00 3.86
802 835 1.149101 TTTGCCCTTCTCTGGTCCTT 58.851 50.000 0.00 0.00 0.00 3.36
804 837 0.693049 TGCCCTTCTCTGGTCCTTTC 59.307 55.000 0.00 0.00 0.00 2.62
838 871 2.739379 CCTTTTCCACTCTCGAAGCTTC 59.261 50.000 16.84 16.84 0.00 3.86
848 881 1.795286 CTCGAAGCTTCAACCTCACAC 59.205 52.381 25.47 0.00 0.00 3.82
853 886 1.002544 AGCTTCAACCTCACACTAGCC 59.997 52.381 0.00 0.00 0.00 3.93
856 889 0.321671 TCAACCTCACACTAGCCAGC 59.678 55.000 0.00 0.00 0.00 4.85
857 890 0.674895 CAACCTCACACTAGCCAGCC 60.675 60.000 0.00 0.00 0.00 4.85
858 891 1.842381 AACCTCACACTAGCCAGCCC 61.842 60.000 0.00 0.00 0.00 5.19
859 892 2.586792 CTCACACTAGCCAGCCCC 59.413 66.667 0.00 0.00 0.00 5.80
860 893 2.203922 TCACACTAGCCAGCCCCA 60.204 61.111 0.00 0.00 0.00 4.96
861 894 2.249413 CTCACACTAGCCAGCCCCAG 62.249 65.000 0.00 0.00 0.00 4.45
862 895 2.122729 ACACTAGCCAGCCCCAGA 59.877 61.111 0.00 0.00 0.00 3.86
1399 1444 4.836825 TGGCGATTTTTCTTGAGATCTCT 58.163 39.130 22.95 0.19 0.00 3.10
1400 1445 4.872691 TGGCGATTTTTCTTGAGATCTCTC 59.127 41.667 22.95 8.96 43.15 3.20
1403 1448 4.026145 CGATTTTTCTTGAGATCTCTCGCC 60.026 45.833 22.95 0.00 45.72 5.54
1432 1477 7.812690 AGCATTTTAGCATCAGTGATGATTA 57.187 32.000 32.61 20.18 42.09 1.75
1519 1564 1.131303 TGGAGAAATGGGGTCGTGGT 61.131 55.000 0.00 0.00 0.00 4.16
1534 1579 4.320348 GGTCGTGGTATCTGTATGTAGCTC 60.320 50.000 0.00 0.00 0.00 4.09
1535 1580 3.497262 TCGTGGTATCTGTATGTAGCTCG 59.503 47.826 0.00 0.00 36.93 5.03
1588 1633 6.644181 TGATTTAATTTGTTCGCATTTGCTCA 59.356 30.769 0.51 0.00 39.32 4.26
1674 1719 1.519898 CTGCAATTTGATGCCCGGC 60.520 57.895 1.04 1.04 45.83 6.13
1720 1769 5.116074 GTCAATGCTCAGTTCATTGTTTTCG 59.884 40.000 13.32 0.00 46.50 3.46
1964 2029 7.891561 TGTTCCAACCCAAATGATTACTTTAG 58.108 34.615 0.00 0.00 0.00 1.85
1967 2032 6.435904 TCCAACCCAAATGATTACTTTAGGTG 59.564 38.462 0.00 0.00 0.00 4.00
1969 2034 4.398044 ACCCAAATGATTACTTTAGGTGCG 59.602 41.667 0.00 0.00 0.00 5.34
2044 2109 7.433719 GCTGTAAACTATGAGTCAGTATCACAG 59.566 40.741 14.48 14.48 34.99 3.66
2045 2110 8.575649 TGTAAACTATGAGTCAGTATCACAGA 57.424 34.615 0.00 0.00 0.00 3.41
2046 2111 9.190317 TGTAAACTATGAGTCAGTATCACAGAT 57.810 33.333 0.00 0.00 0.00 2.90
2050 2115 9.634021 AACTATGAGTCAGTATCACAGATAAGA 57.366 33.333 0.00 0.00 0.00 2.10
2051 2116 9.806448 ACTATGAGTCAGTATCACAGATAAGAT 57.194 33.333 0.00 0.00 0.00 2.40
2199 2264 6.481313 CAGTCAAGGTGGATTCTATATGTGTG 59.519 42.308 0.00 0.00 0.00 3.82
2260 2325 7.246674 TGTCATGGATATCTTTTTAAGTCGC 57.753 36.000 2.05 0.00 0.00 5.19
2321 2386 6.096673 TGCTTGCTAATCGTCATTATCCTA 57.903 37.500 0.00 0.00 0.00 2.94
2344 2409 9.892130 CCTATTTGAAGACTATCCTTACTTTGT 57.108 33.333 0.00 0.00 0.00 2.83
2348 2413 9.924650 TTTGAAGACTATCCTTACTTTGTACTC 57.075 33.333 0.00 0.00 0.00 2.59
2349 2414 8.064336 TGAAGACTATCCTTACTTTGTACTCC 57.936 38.462 0.00 0.00 0.00 3.85
2350 2415 7.123847 TGAAGACTATCCTTACTTTGTACTCCC 59.876 40.741 0.00 0.00 0.00 4.30
2351 2416 6.743788 AGACTATCCTTACTTTGTACTCCCT 58.256 40.000 0.00 0.00 0.00 4.20
2352 2417 6.834969 AGACTATCCTTACTTTGTACTCCCTC 59.165 42.308 0.00 0.00 0.00 4.30
2353 2418 5.898397 ACTATCCTTACTTTGTACTCCCTCC 59.102 44.000 0.00 0.00 0.00 4.30
2354 2419 3.094572 TCCTTACTTTGTACTCCCTCCG 58.905 50.000 0.00 0.00 0.00 4.63
2355 2420 2.830321 CCTTACTTTGTACTCCCTCCGT 59.170 50.000 0.00 0.00 0.00 4.69
2356 2421 3.119209 CCTTACTTTGTACTCCCTCCGTC 60.119 52.174 0.00 0.00 0.00 4.79
2357 2422 1.264295 ACTTTGTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
2358 2423 0.535797 CTTTGTACTCCCTCCGTCCC 59.464 60.000 0.00 0.00 0.00 4.46
2359 2424 0.178926 TTTGTACTCCCTCCGTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
2360 2425 0.042131 TTGTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00
2361 2426 0.928505 TGTACTCCCTCCGTCCCATA 59.071 55.000 0.00 0.00 0.00 2.74
2362 2427 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90
2363 2428 2.090943 TGTACTCCCTCCGTCCCATAAT 60.091 50.000 0.00 0.00 0.00 1.28
2364 2429 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2365 2430 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2366 2431 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2367 2432 2.563179 CTCCCTCCGTCCCATAATGTAG 59.437 54.545 0.00 0.00 0.00 2.74
2368 2433 1.623811 CCCTCCGTCCCATAATGTAGG 59.376 57.143 0.00 0.00 0.00 3.18
2369 2434 2.605257 CCTCCGTCCCATAATGTAGGA 58.395 52.381 0.00 0.00 0.00 2.94
2370 2435 3.173965 CCTCCGTCCCATAATGTAGGAT 58.826 50.000 0.00 0.00 30.92 3.24
2371 2436 3.055819 CCTCCGTCCCATAATGTAGGATG 60.056 52.174 0.00 0.00 36.59 3.51
2372 2437 3.578716 CTCCGTCCCATAATGTAGGATGT 59.421 47.826 0.00 0.00 35.30 3.06
2373 2438 3.971305 TCCGTCCCATAATGTAGGATGTT 59.029 43.478 0.00 0.00 35.30 2.71
2374 2439 4.410883 TCCGTCCCATAATGTAGGATGTTT 59.589 41.667 0.00 0.00 35.30 2.83
2375 2440 5.104277 TCCGTCCCATAATGTAGGATGTTTT 60.104 40.000 0.00 0.00 35.30 2.43
2376 2441 5.592688 CCGTCCCATAATGTAGGATGTTTTT 59.407 40.000 0.00 0.00 35.30 1.94
2397 2462 7.867305 TTTTTCACACCAGTATAGTGTCAAA 57.133 32.000 6.81 0.00 45.13 2.69
2398 2463 7.867305 TTTTCACACCAGTATAGTGTCAAAA 57.133 32.000 6.81 2.35 45.13 2.44
2399 2464 7.867305 TTTCACACCAGTATAGTGTCAAAAA 57.133 32.000 6.81 0.89 45.13 1.94
2400 2465 7.490962 TTCACACCAGTATAGTGTCAAAAAG 57.509 36.000 6.81 0.00 45.13 2.27
2401 2466 5.468746 TCACACCAGTATAGTGTCAAAAAGC 59.531 40.000 6.81 0.00 45.13 3.51
2402 2467 4.451096 ACACCAGTATAGTGTCAAAAAGCG 59.549 41.667 6.81 0.00 45.13 4.68
2403 2468 4.451096 CACCAGTATAGTGTCAAAAAGCGT 59.549 41.667 6.81 0.00 0.00 5.07
2404 2469 4.689345 ACCAGTATAGTGTCAAAAAGCGTC 59.311 41.667 6.81 0.00 0.00 5.19
2405 2470 4.929808 CCAGTATAGTGTCAAAAAGCGTCT 59.070 41.667 6.81 0.00 0.00 4.18
2406 2471 5.408604 CCAGTATAGTGTCAAAAAGCGTCTT 59.591 40.000 6.81 0.00 0.00 3.01
2407 2472 6.588756 CCAGTATAGTGTCAAAAAGCGTCTTA 59.411 38.462 6.81 0.00 0.00 2.10
2408 2473 7.411588 CCAGTATAGTGTCAAAAAGCGTCTTAC 60.412 40.741 6.81 0.00 0.00 2.34
2409 2474 7.115805 CAGTATAGTGTCAAAAAGCGTCTTACA 59.884 37.037 0.00 0.00 0.00 2.41
2410 2475 7.817962 AGTATAGTGTCAAAAAGCGTCTTACAT 59.182 33.333 0.00 0.00 0.00 2.29
2411 2476 5.751243 AGTGTCAAAAAGCGTCTTACATT 57.249 34.783 0.00 0.00 0.00 2.71
2412 2477 6.854496 AGTGTCAAAAAGCGTCTTACATTA 57.146 33.333 0.00 0.00 0.00 1.90
2413 2478 7.435068 AGTGTCAAAAAGCGTCTTACATTAT 57.565 32.000 0.00 0.00 0.00 1.28
2414 2479 7.298122 AGTGTCAAAAAGCGTCTTACATTATG 58.702 34.615 0.00 0.00 0.00 1.90
2415 2480 6.523201 GTGTCAAAAAGCGTCTTACATTATGG 59.477 38.462 0.00 0.00 0.00 2.74
2416 2481 6.027749 GTCAAAAAGCGTCTTACATTATGGG 58.972 40.000 0.00 0.00 0.00 4.00
2417 2482 5.941058 TCAAAAAGCGTCTTACATTATGGGA 59.059 36.000 0.00 0.00 0.00 4.37
2418 2483 5.813080 AAAAGCGTCTTACATTATGGGAC 57.187 39.130 0.00 1.75 0.00 4.46
2497 2562 6.830324 TGATCAAATTCTGCTTTAGGCTATGT 59.170 34.615 0.00 0.00 42.39 2.29
2530 2599 6.238759 GGAACAATTGTACTCAGCTTTCTGTT 60.239 38.462 12.39 0.00 41.10 3.16
2541 2610 6.825721 ACTCAGCTTTCTGTTAATAATCCCTG 59.174 38.462 0.00 0.00 41.10 4.45
2661 2730 5.810525 ACTCTTTGTTTTTCACTGATCACG 58.189 37.500 0.00 0.00 0.00 4.35
2697 2766 9.733556 TCAGAAGATTTGCTAATTTAGGTTACA 57.266 29.630 5.61 0.00 0.00 2.41
2708 2777 8.953990 GCTAATTTAGGTTACAATAATGTTGCG 58.046 33.333 5.61 0.00 41.05 4.85
2726 2798 3.194861 TGCGCTAAGTTATGATGGTGTC 58.805 45.455 9.73 0.00 0.00 3.67
2741 2813 7.359262 TGATGGTGTCGTAGATAAAAACTTG 57.641 36.000 0.00 0.00 40.67 3.16
2757 2829 5.869753 AAACTTGCATGTGTGATAGTCTC 57.130 39.130 5.94 0.00 0.00 3.36
2793 2865 8.531622 TTTGCCAAATTTCATGTACAATAGTG 57.468 30.769 0.00 0.00 0.00 2.74
2821 2893 2.684943 TCTTTGTAGTCCTGGGTGACA 58.315 47.619 0.00 0.00 37.73 3.58
2898 2977 1.762419 TACTTGTTGACTGCGTCGAC 58.238 50.000 17.09 17.09 44.65 4.20
3002 3082 4.574421 TGTCATACGTTATTCCAGCAATGG 59.426 41.667 0.00 0.00 0.00 3.16
3442 3522 0.609662 CAAGGGCATTCAACCAAGGG 59.390 55.000 0.00 0.00 0.00 3.95
3545 3625 4.604156 TCTTGATGAGGAGCAGAAGAGTA 58.396 43.478 0.00 0.00 29.91 2.59
3546 3626 4.400884 TCTTGATGAGGAGCAGAAGAGTAC 59.599 45.833 0.00 0.00 29.91 2.73
3547 3627 3.027412 TGATGAGGAGCAGAAGAGTACC 58.973 50.000 0.00 0.00 0.00 3.34
3586 3666 0.461961 GACACTGGGGGATCTTCTCG 59.538 60.000 0.00 0.00 0.00 4.04
3595 3675 2.565841 GGGATCTTCTCGTTTGATGGG 58.434 52.381 0.00 0.00 0.00 4.00
3712 3792 4.177229 GCTCAGAGCCTCGACAAC 57.823 61.111 11.84 0.00 34.48 3.32
3725 3805 1.563173 GACAACGCGTCAACTCACC 59.437 57.895 14.44 0.00 44.69 4.02
3808 3888 2.046217 GGGGAGAAGGGCAACGTC 60.046 66.667 0.00 0.00 37.60 4.34
3865 3945 0.917533 AGGATGCCAAGAGCTGTGAT 59.082 50.000 0.00 0.00 44.23 3.06
3881 3961 0.831966 TGATTTTGATGGGCATGGGC 59.168 50.000 0.00 0.00 40.13 5.36
3904 3984 6.060788 GCTGATAACTTTCCTTGATCCATCT 58.939 40.000 0.00 0.00 0.00 2.90
3967 4047 1.302033 CTCTGCGGTTGCCTCTTGT 60.302 57.895 0.00 0.00 41.78 3.16
3979 4059 0.963962 CCTCTTGTGGCAATTGCTGT 59.036 50.000 28.42 0.00 41.70 4.40
4007 4087 0.796312 CTGTGGGGTGTCGATTTTCG 59.204 55.000 0.00 0.00 42.10 3.46
4016 4096 1.944024 TGTCGATTTTCGCTTTGTGGT 59.056 42.857 0.00 0.00 40.21 4.16
4040 4120 6.806668 TGTTCATGTACCTTAGGATGATGA 57.193 37.500 4.77 6.05 0.00 2.92
4052 4132 1.348366 GGATGATGAGCTCTGCCTGAT 59.652 52.381 16.19 0.00 0.00 2.90
4054 4134 0.468648 TGATGAGCTCTGCCTGATGG 59.531 55.000 16.19 0.00 0.00 3.51
4056 4136 0.917533 ATGAGCTCTGCCTGATGGTT 59.082 50.000 16.19 0.00 35.27 3.67
4063 4143 3.349927 CTCTGCCTGATGGTTGAAATGA 58.650 45.455 0.00 0.00 35.27 2.57
4067 4147 5.104402 TCTGCCTGATGGTTGAAATGATCTA 60.104 40.000 0.00 0.00 35.27 1.98
4251 6019 9.988815 ATTTCTATCTGCCAGTAGTAATACTTG 57.011 33.333 0.00 0.00 0.00 3.16
4252 6020 6.982852 TCTATCTGCCAGTAGTAATACTTGC 58.017 40.000 16.92 16.92 38.68 4.01
4253 6021 5.878406 ATCTGCCAGTAGTAATACTTGCT 57.122 39.130 22.15 4.83 38.89 3.91
4254 6022 5.011090 TCTGCCAGTAGTAATACTTGCTG 57.989 43.478 22.15 21.14 38.89 4.41
4255 6023 3.531538 TGCCAGTAGTAATACTTGCTGC 58.468 45.455 22.15 13.29 38.89 5.25
4256 6024 3.055458 TGCCAGTAGTAATACTTGCTGCA 60.055 43.478 22.15 15.20 38.89 4.41
4257 6025 3.309954 GCCAGTAGTAATACTTGCTGCAC 59.690 47.826 16.59 8.52 36.25 4.57
4258 6026 4.759782 CCAGTAGTAATACTTGCTGCACT 58.240 43.478 0.00 0.00 32.46 4.40
4259 6027 5.681437 GCCAGTAGTAATACTTGCTGCACTA 60.681 44.000 16.59 0.00 36.25 2.74
4260 6028 5.980116 CCAGTAGTAATACTTGCTGCACTAG 59.020 44.000 0.00 0.00 32.46 2.57
4261 6029 6.405953 CCAGTAGTAATACTTGCTGCACTAGT 60.406 42.308 11.35 11.35 38.03 2.57
4262 6030 7.036220 CAGTAGTAATACTTGCTGCACTAGTT 58.964 38.462 11.81 3.99 35.82 2.24
4263 6031 7.545965 CAGTAGTAATACTTGCTGCACTAGTTT 59.454 37.037 11.81 8.85 35.82 2.66
4264 6032 8.746530 AGTAGTAATACTTGCTGCACTAGTTTA 58.253 33.333 11.81 8.08 35.82 2.01
4265 6033 9.021863 GTAGTAATACTTGCTGCACTAGTTTAG 57.978 37.037 11.81 3.23 35.82 1.85
4266 6034 7.837863 AGTAATACTTGCTGCACTAGTTTAGA 58.162 34.615 11.81 0.00 35.82 2.10
4267 6035 8.478877 AGTAATACTTGCTGCACTAGTTTAGAT 58.521 33.333 11.81 0.00 35.82 1.98
4268 6036 9.099454 GTAATACTTGCTGCACTAGTTTAGATT 57.901 33.333 11.81 8.33 35.82 2.40
4270 6038 8.879342 ATACTTGCTGCACTAGTTTAGATTAG 57.121 34.615 11.81 0.43 35.82 1.73
4271 6039 6.936279 ACTTGCTGCACTAGTTTAGATTAGA 58.064 36.000 0.00 0.00 29.37 2.10
4272 6040 7.038659 ACTTGCTGCACTAGTTTAGATTAGAG 58.961 38.462 0.00 0.00 29.37 2.43
4273 6041 5.907207 TGCTGCACTAGTTTAGATTAGAGG 58.093 41.667 0.00 0.00 0.00 3.69
4274 6042 5.656859 TGCTGCACTAGTTTAGATTAGAGGA 59.343 40.000 0.00 0.00 0.00 3.71
4275 6043 5.980715 GCTGCACTAGTTTAGATTAGAGGAC 59.019 44.000 7.21 0.00 0.00 3.85
4276 6044 6.405953 GCTGCACTAGTTTAGATTAGAGGACA 60.406 42.308 7.21 0.00 0.00 4.02
4277 6045 7.476540 TGCACTAGTTTAGATTAGAGGACAA 57.523 36.000 0.00 0.00 0.00 3.18
4278 6046 7.548097 TGCACTAGTTTAGATTAGAGGACAAG 58.452 38.462 0.00 0.00 0.00 3.16
4290 6058 3.577919 AGAGGACAAGTGGTGAGTAGTT 58.422 45.455 0.00 0.00 0.00 2.24
4318 6086 4.558226 TGATGTAGCACCTGAATGAAGT 57.442 40.909 0.00 0.00 0.00 3.01
4361 6129 5.086621 AGGGATGTTTATTGCTGGAAAGTT 58.913 37.500 0.00 0.00 0.00 2.66
4370 6138 8.613482 GTTTATTGCTGGAAAGTTATAGAGACC 58.387 37.037 0.00 0.00 0.00 3.85
4466 6243 1.089920 CTTCCGATGAACAAGCCTGG 58.910 55.000 0.00 0.00 0.00 4.45
4482 6261 0.171903 CTGGGCATCCTTTTTCAGCG 59.828 55.000 0.00 0.00 0.00 5.18
4486 6265 0.733909 GCATCCTTTTTCAGCGTGCC 60.734 55.000 0.00 0.00 0.00 5.01
4489 6268 1.082104 CCTTTTTCAGCGTGCCGAC 60.082 57.895 0.00 0.00 0.00 4.79
4616 6395 1.601759 GCAAGGTGAAGCTCAGCCA 60.602 57.895 0.00 0.00 45.34 4.75
4617 6396 1.174712 GCAAGGTGAAGCTCAGCCAA 61.175 55.000 0.00 0.00 45.34 4.52
4618 6397 1.321474 CAAGGTGAAGCTCAGCCAAA 58.679 50.000 0.00 0.00 45.34 3.28
4658 6437 0.736636 ATGATGTGAGCATGCCAACG 59.263 50.000 15.66 0.00 35.07 4.10
4684 6475 5.464030 TGACTGTCTAACTAACCAAGGTC 57.536 43.478 9.51 0.00 0.00 3.85
4700 6496 4.261614 CCAAGGTCGAAAAGAAAAAGGAGG 60.262 45.833 0.00 0.00 0.00 4.30
4713 6509 0.988063 AAGGAGGGAAGAGCTGAACC 59.012 55.000 0.00 0.00 0.00 3.62
4746 6542 0.105964 TTACGCAGTGAAGCAGTGGT 59.894 50.000 0.00 0.00 45.73 4.16
4833 6629 2.158475 TCCTCATGCCTCCTGTTTTGTT 60.158 45.455 0.00 0.00 0.00 2.83
4840 6636 2.813061 CCTCCTGTTTTGTTTGCTGTG 58.187 47.619 0.00 0.00 0.00 3.66
4881 6677 0.674895 CGGTTCAGAGCTTTCAGGGG 60.675 60.000 0.00 0.00 0.00 4.79
4882 6678 0.693049 GGTTCAGAGCTTTCAGGGGA 59.307 55.000 0.00 0.00 0.00 4.81
4901 6697 2.092211 GGAGATCTACGTGTTTGCAACG 59.908 50.000 7.83 7.83 0.00 4.10
4966 6821 3.785486 TGGCTCGACTTGTGATAAGATG 58.215 45.455 0.00 0.00 0.00 2.90
4995 6850 0.040067 CGCTTTGCTTGACTTGGACC 60.040 55.000 0.00 0.00 0.00 4.46
4998 6853 1.264288 CTTTGCTTGACTTGGACCGAC 59.736 52.381 0.00 0.00 0.00 4.79
5046 6901 0.250252 TTGGACTTGACATCGCAGCA 60.250 50.000 0.00 0.00 0.00 4.41
5047 6902 0.950555 TGGACTTGACATCGCAGCAC 60.951 55.000 0.00 0.00 0.00 4.40
5048 6903 0.950555 GGACTTGACATCGCAGCACA 60.951 55.000 0.00 0.00 0.00 4.57
5049 6904 1.081892 GACTTGACATCGCAGCACAT 58.918 50.000 0.00 0.00 0.00 3.21
5050 6905 0.800631 ACTTGACATCGCAGCACATG 59.199 50.000 0.00 0.00 0.00 3.21
5051 6906 0.800631 CTTGACATCGCAGCACATGT 59.199 50.000 6.67 6.67 35.88 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 2.683933 TCCTCTCCAAGGCCGACC 60.684 66.667 0.00 0.00 45.78 4.79
184 185 0.109086 CCGACGAGCAATGACTGAGT 60.109 55.000 0.00 0.00 0.00 3.41
218 225 2.282462 CCACAGAAGCACACCCCC 60.282 66.667 0.00 0.00 0.00 5.40
220 227 0.886490 CTCACCACAGAAGCACACCC 60.886 60.000 0.00 0.00 0.00 4.61
223 230 0.249447 CGTCTCACCACAGAAGCACA 60.249 55.000 0.00 0.00 0.00 4.57
224 231 0.032130 TCGTCTCACCACAGAAGCAC 59.968 55.000 0.00 0.00 0.00 4.40
254 264 2.326550 GTGAACGCCACAACCACG 59.673 61.111 3.95 0.00 45.03 4.94
274 284 0.702316 ATAAAAGTTGGCCTCCCCGT 59.298 50.000 3.32 0.00 35.87 5.28
285 295 3.195661 CCTCGCTTCGGCTATAAAAGTT 58.804 45.455 0.00 0.00 39.13 2.66
394 406 2.671070 CCGGTCAGCCTCCATTGT 59.329 61.111 0.00 0.00 0.00 2.71
419 431 4.802051 ATGCCAAGGATGCCGCGT 62.802 61.111 4.92 0.00 0.00 6.01
427 441 1.037030 GCGGGAATCAATGCCAAGGA 61.037 55.000 0.00 0.00 40.15 3.36
495 509 0.612732 ACGTGAACGGGGATAGGTCA 60.613 55.000 7.86 0.00 44.95 4.02
497 511 0.612732 TGACGTGAACGGGGATAGGT 60.613 55.000 7.86 0.00 44.95 3.08
500 514 2.415776 GTTTTGACGTGAACGGGGATA 58.584 47.619 7.86 0.00 44.95 2.59
511 525 0.382873 GGGAAAAGCGGTTTTGACGT 59.617 50.000 28.28 5.45 35.94 4.34
544 561 0.691904 AACCCAAACCGAACCCGATA 59.308 50.000 0.00 0.00 38.22 2.92
546 563 1.227913 GAACCCAAACCGAACCCGA 60.228 57.895 0.00 0.00 38.22 5.14
563 580 4.951254 TGAATCGAAACTAGTGTTGGTGA 58.049 39.130 0.00 0.00 36.39 4.02
565 582 5.008316 GGTTTGAATCGAAACTAGTGTTGGT 59.992 40.000 0.00 0.00 36.30 3.67
568 585 4.212636 CCGGTTTGAATCGAAACTAGTGTT 59.787 41.667 0.00 0.00 36.30 3.32
573 590 2.078392 GGCCGGTTTGAATCGAAACTA 58.922 47.619 1.90 0.00 36.30 2.24
581 598 1.137282 ACGTTTTTGGCCGGTTTGAAT 59.863 42.857 1.90 0.00 0.00 2.57
582 599 0.531200 ACGTTTTTGGCCGGTTTGAA 59.469 45.000 1.90 0.00 0.00 2.69
583 600 0.179134 CACGTTTTTGGCCGGTTTGA 60.179 50.000 1.90 0.00 0.00 2.69
593 610 5.288232 TCATGTTTTCAAGAGCACGTTTTTG 59.712 36.000 0.00 0.00 0.00 2.44
601 618 2.294233 GCCAGTCATGTTTTCAAGAGCA 59.706 45.455 0.00 0.00 0.00 4.26
606 623 6.418057 AAAATAGGCCAGTCATGTTTTCAA 57.582 33.333 5.01 0.00 26.15 2.69
705 726 0.824109 CCTACAGAGCCGTTGGATCA 59.176 55.000 3.70 0.00 41.08 2.92
706 727 0.530870 GCCTACAGAGCCGTTGGATC 60.531 60.000 3.71 0.00 38.56 3.36
707 728 1.522569 GCCTACAGAGCCGTTGGAT 59.477 57.895 3.71 0.00 34.13 3.41
718 740 2.119495 AGGGTTGACATAGGCCTACAG 58.881 52.381 16.61 13.58 0.00 2.74
723 745 1.453928 GGCAGGGTTGACATAGGCC 60.454 63.158 0.00 0.00 30.39 5.19
729 751 3.825160 GAGCGTGGCAGGGTTGACA 62.825 63.158 13.53 0.00 41.02 3.58
766 794 6.668645 AGGGCAAATAGGTCAATATACAACA 58.331 36.000 0.00 0.00 0.00 3.33
797 825 2.820197 GGTGGGTGAAATCTGAAAGGAC 59.180 50.000 0.00 0.00 0.00 3.85
802 835 3.895041 GGAAAAGGTGGGTGAAATCTGAA 59.105 43.478 0.00 0.00 0.00 3.02
804 837 3.005791 GTGGAAAAGGTGGGTGAAATCTG 59.994 47.826 0.00 0.00 0.00 2.90
838 871 0.674895 GGCTGGCTAGTGTGAGGTTG 60.675 60.000 0.00 0.00 0.00 3.77
848 881 3.483869 GGGTCTGGGGCTGGCTAG 61.484 72.222 0.00 0.00 0.00 3.42
853 886 3.406200 CTCTGGGGTCTGGGGCTG 61.406 72.222 0.00 0.00 0.00 4.85
856 889 2.612115 AAGCTCTGGGGTCTGGGG 60.612 66.667 0.00 0.00 0.00 4.96
857 890 1.908340 CTGAAGCTCTGGGGTCTGGG 61.908 65.000 0.00 0.00 0.00 4.45
858 891 1.601171 CTGAAGCTCTGGGGTCTGG 59.399 63.158 0.00 0.00 0.00 3.86
859 892 1.078567 GCTGAAGCTCTGGGGTCTG 60.079 63.158 0.00 0.00 38.21 3.51
860 893 3.397906 GCTGAAGCTCTGGGGTCT 58.602 61.111 0.00 0.00 38.21 3.85
884 917 2.882137 GAGAGGAGGACGAAGATAGTGG 59.118 54.545 0.00 0.00 0.00 4.00
885 918 3.546724 TGAGAGGAGGACGAAGATAGTG 58.453 50.000 0.00 0.00 0.00 2.74
1341 1385 1.514228 CACTCACCGGATGTCGACG 60.514 63.158 9.46 0.00 42.43 5.12
1399 1444 0.446222 GCTAAAATGCTTCACGGCGA 59.554 50.000 16.62 0.00 34.52 5.54
1400 1445 0.167908 TGCTAAAATGCTTCACGGCG 59.832 50.000 4.80 4.80 34.52 6.46
1403 1448 4.093514 CACTGATGCTAAAATGCTTCACG 58.906 43.478 0.00 0.00 40.55 4.35
1432 1477 7.343357 TCAAGTAACAGGAATCCCGAAATAAT 58.657 34.615 0.00 0.00 37.58 1.28
1519 1564 4.969484 TCCACTCGAGCTACATACAGATA 58.031 43.478 13.61 0.00 0.00 1.98
1534 1579 2.290323 ACCAGATTCCCTTTTCCACTCG 60.290 50.000 0.00 0.00 0.00 4.18
1535 1580 3.084786 CACCAGATTCCCTTTTCCACTC 58.915 50.000 0.00 0.00 0.00 3.51
1588 1633 4.292186 TCAATTGAACTAAGCAGCTCCT 57.708 40.909 5.45 0.00 0.00 3.69
1967 2032 2.117156 ATGGCAGGTGATTCAGCGC 61.117 57.895 18.04 18.04 36.92 5.92
1969 2034 1.022735 CTCATGGCAGGTGATTCAGC 58.977 55.000 7.79 7.79 0.00 4.26
2018 2083 7.258441 TGTGATACTGACTCATAGTTTACAGC 58.742 38.462 0.00 0.00 0.00 4.40
2119 2184 4.583073 ACTTCCAAGTTCCAACAACATACC 59.417 41.667 0.00 0.00 35.21 2.73
2260 2325 2.438434 GGCTCACATCAACCCCGG 60.438 66.667 0.00 0.00 0.00 5.73
2342 2407 0.928505 TATGGGACGGAGGGAGTACA 59.071 55.000 0.00 0.00 0.00 2.90
2343 2408 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
2344 2409 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
2345 2410 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
2346 2411 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2347 2412 2.605257 CTACATTATGGGACGGAGGGA 58.395 52.381 0.00 0.00 0.00 4.20
2348 2413 1.623811 CCTACATTATGGGACGGAGGG 59.376 57.143 0.00 0.00 0.00 4.30
2349 2414 2.605257 TCCTACATTATGGGACGGAGG 58.395 52.381 0.00 0.00 31.72 4.30
2350 2415 3.578716 ACATCCTACATTATGGGACGGAG 59.421 47.826 0.00 0.00 41.57 4.63
2351 2416 3.583228 ACATCCTACATTATGGGACGGA 58.417 45.455 0.00 0.00 41.57 4.69
2352 2417 4.351874 AACATCCTACATTATGGGACGG 57.648 45.455 0.00 0.00 41.57 4.79
2353 2418 6.693315 AAAAACATCCTACATTATGGGACG 57.307 37.500 0.00 0.00 41.57 4.79
2373 2438 7.867305 TTTGACACTATACTGGTGTGAAAAA 57.133 32.000 8.58 3.37 43.57 1.94
2375 2440 7.468084 GCTTTTTGACACTATACTGGTGTGAAA 60.468 37.037 4.18 5.95 46.23 2.69
2376 2441 6.017440 GCTTTTTGACACTATACTGGTGTGAA 60.017 38.462 4.18 0.00 46.23 3.18
2377 2442 5.468746 GCTTTTTGACACTATACTGGTGTGA 59.531 40.000 4.18 0.00 46.23 3.58
2378 2443 5.614668 CGCTTTTTGACACTATACTGGTGTG 60.615 44.000 4.18 0.00 46.23 3.82
2380 2445 4.451096 ACGCTTTTTGACACTATACTGGTG 59.549 41.667 0.00 0.00 40.19 4.17
2381 2446 4.638304 ACGCTTTTTGACACTATACTGGT 58.362 39.130 0.00 0.00 0.00 4.00
2382 2447 4.929808 AGACGCTTTTTGACACTATACTGG 59.070 41.667 0.00 0.00 0.00 4.00
2383 2448 6.467723 AAGACGCTTTTTGACACTATACTG 57.532 37.500 0.00 0.00 0.00 2.74
2384 2449 7.149973 TGTAAGACGCTTTTTGACACTATACT 58.850 34.615 0.00 0.00 0.00 2.12
2385 2450 7.342318 TGTAAGACGCTTTTTGACACTATAC 57.658 36.000 0.00 0.00 0.00 1.47
2386 2451 8.542497 AATGTAAGACGCTTTTTGACACTATA 57.458 30.769 0.00 0.00 0.00 1.31
2387 2452 7.435068 AATGTAAGACGCTTTTTGACACTAT 57.565 32.000 0.00 0.00 0.00 2.12
2388 2453 6.854496 AATGTAAGACGCTTTTTGACACTA 57.146 33.333 0.00 0.00 0.00 2.74
2389 2454 5.751243 AATGTAAGACGCTTTTTGACACT 57.249 34.783 0.00 0.00 0.00 3.55
2390 2455 6.523201 CCATAATGTAAGACGCTTTTTGACAC 59.477 38.462 0.00 0.00 0.00 3.67
2391 2456 6.348950 CCCATAATGTAAGACGCTTTTTGACA 60.349 38.462 0.00 0.00 0.00 3.58
2392 2457 6.027749 CCCATAATGTAAGACGCTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
2393 2458 5.941058 TCCCATAATGTAAGACGCTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
2394 2459 6.027749 GTCCCATAATGTAAGACGCTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
2395 2460 5.708230 TGTCCCATAATGTAAGACGCTTTTT 59.292 36.000 0.00 0.00 0.00 1.94
2396 2461 5.250200 TGTCCCATAATGTAAGACGCTTTT 58.750 37.500 0.00 0.00 0.00 2.27
2397 2462 4.839121 TGTCCCATAATGTAAGACGCTTT 58.161 39.130 0.00 0.00 0.00 3.51
2398 2463 4.161565 TCTGTCCCATAATGTAAGACGCTT 59.838 41.667 0.00 0.00 0.00 4.68
2399 2464 3.704566 TCTGTCCCATAATGTAAGACGCT 59.295 43.478 0.00 0.00 0.00 5.07
2400 2465 4.051922 CTCTGTCCCATAATGTAAGACGC 58.948 47.826 0.00 0.00 0.00 5.19
2401 2466 4.501571 CCCTCTGTCCCATAATGTAAGACG 60.502 50.000 0.00 0.00 0.00 4.18
2402 2467 4.654262 TCCCTCTGTCCCATAATGTAAGAC 59.346 45.833 0.00 0.00 0.00 3.01
2403 2468 4.890988 TCCCTCTGTCCCATAATGTAAGA 58.109 43.478 0.00 0.00 0.00 2.10
2404 2469 4.656112 ACTCCCTCTGTCCCATAATGTAAG 59.344 45.833 0.00 0.00 0.00 2.34
2405 2470 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
2406 2471 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
2407 2472 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
2408 2473 3.967326 TGTACTCCCTCTGTCCCATAATG 59.033 47.826 0.00 0.00 0.00 1.90
2409 2474 4.280789 TGTACTCCCTCTGTCCCATAAT 57.719 45.455 0.00 0.00 0.00 1.28
2410 2475 3.769189 TGTACTCCCTCTGTCCCATAA 57.231 47.619 0.00 0.00 0.00 1.90
2411 2476 3.993658 ATGTACTCCCTCTGTCCCATA 57.006 47.619 0.00 0.00 0.00 2.74
2412 2477 2.877154 ATGTACTCCCTCTGTCCCAT 57.123 50.000 0.00 0.00 0.00 4.00
2413 2478 2.642171 AATGTACTCCCTCTGTCCCA 57.358 50.000 0.00 0.00 0.00 4.37
2414 2479 3.371965 TGTAATGTACTCCCTCTGTCCC 58.628 50.000 0.00 0.00 0.00 4.46
2415 2480 5.128827 TCAATGTAATGTACTCCCTCTGTCC 59.871 44.000 0.00 0.00 0.00 4.02
2416 2481 6.222038 TCAATGTAATGTACTCCCTCTGTC 57.778 41.667 0.00 0.00 0.00 3.51
2417 2482 6.620877 TTCAATGTAATGTACTCCCTCTGT 57.379 37.500 0.00 0.00 0.00 3.41
2418 2483 7.331026 TCTTTCAATGTAATGTACTCCCTCTG 58.669 38.462 0.00 0.00 0.00 3.35
2419 2484 7.496346 TCTTTCAATGTAATGTACTCCCTCT 57.504 36.000 0.00 0.00 0.00 3.69
2420 2485 8.738645 AATCTTTCAATGTAATGTACTCCCTC 57.261 34.615 0.00 0.00 0.00 4.30
2497 2562 4.225492 TGAGTACAATTGTTCCCGGGATTA 59.775 41.667 27.48 14.08 0.00 1.75
2530 2599 4.262635 GCTAGCAGCAGACAGGGATTATTA 60.263 45.833 10.63 0.00 41.89 0.98
2573 2642 7.187824 AGGCACTCAAGTAGAATTTCTGATA 57.812 36.000 9.22 0.00 0.00 2.15
2632 2701 7.873719 TCAGTGAAAAACAAAGAGTATCCAA 57.126 32.000 0.00 0.00 33.66 3.53
2661 2730 6.218108 AGCAAATCTTCTGAATCCAAATCC 57.782 37.500 0.00 0.00 0.00 3.01
2697 2766 7.013274 ACCATCATAACTTAGCGCAACATTATT 59.987 33.333 11.47 0.00 0.00 1.40
2708 2777 5.828747 TCTACGACACCATCATAACTTAGC 58.171 41.667 0.00 0.00 0.00 3.09
2726 2798 6.598525 TCACACATGCAAGTTTTTATCTACG 58.401 36.000 0.00 0.00 0.00 3.51
2741 2813 3.854666 ACACAGAGACTATCACACATGC 58.145 45.455 0.00 0.00 0.00 4.06
2757 2829 9.171701 CATGAAATTTGGCAAATTAAAACACAG 57.828 29.630 31.88 20.78 40.05 3.66
2793 2865 6.763610 CACCCAGGACTACAAAGATCTTATTC 59.236 42.308 8.75 0.00 0.00 1.75
2804 2876 2.615391 TGATGTCACCCAGGACTACAA 58.385 47.619 0.00 0.00 38.61 2.41
2845 2924 3.973206 AACCGAATAGTCATGTGTCCA 57.027 42.857 0.00 0.00 0.00 4.02
3002 3082 2.991190 CCAGTGATTGCTGAATGTTTGC 59.009 45.455 0.00 0.00 38.70 3.68
3499 3579 3.950395 GGCCAAAAAGATAGACATCAGCT 59.050 43.478 0.00 0.00 33.21 4.24
3545 3625 2.224793 GCTCAAAGTTTCCAGGTAGGGT 60.225 50.000 0.00 0.00 38.24 4.34
3546 3626 2.437413 GCTCAAAGTTTCCAGGTAGGG 58.563 52.381 0.00 0.00 38.24 3.53
3547 3627 2.076863 CGCTCAAAGTTTCCAGGTAGG 58.923 52.381 0.00 0.00 39.47 3.18
3586 3666 1.187567 ACTTGGCCTGCCCATCAAAC 61.188 55.000 3.32 0.00 44.89 2.93
3595 3675 0.321830 TTAACGGGTACTTGGCCTGC 60.322 55.000 3.32 0.00 35.84 4.85
3637 3717 3.181502 GCACCTCTTTAGCATTCTTCAGC 60.182 47.826 0.00 0.00 0.00 4.26
3712 3792 1.891060 GCTTCAGGTGAGTTGACGCG 61.891 60.000 3.53 3.53 31.54 6.01
3725 3805 0.520404 ATGTCGCAAGCAAGCTTCAG 59.480 50.000 3.97 2.26 33.42 3.02
3808 3888 3.817647 AGTAGCTGTTGAAAGCAAAGGAG 59.182 43.478 0.00 0.00 46.08 3.69
3865 3945 0.252148 TCAGCCCATGCCCATCAAAA 60.252 50.000 0.00 0.00 38.69 2.44
3881 3961 9.217278 CATAGATGGATCAAGGAAAGTTATCAG 57.783 37.037 0.00 0.00 0.00 2.90
3904 3984 1.064758 AGAAAGCGGCATTCACCCATA 60.065 47.619 18.76 0.00 0.00 2.74
3967 4047 1.907807 GACCCCACAGCAATTGCCA 60.908 57.895 26.45 0.00 43.38 4.92
3971 4051 1.145738 ACAGAAGACCCCACAGCAATT 59.854 47.619 0.00 0.00 0.00 2.32
3979 4059 2.153401 CACCCCACAGAAGACCCCA 61.153 63.158 0.00 0.00 0.00 4.96
4007 4087 3.317993 AGGTACATGAACAACCACAAAGC 59.682 43.478 0.00 0.00 35.64 3.51
4016 4096 7.194112 TCATCATCCTAAGGTACATGAACAA 57.806 36.000 0.00 0.00 0.00 2.83
4040 4120 0.694771 TTCAACCATCAGGCAGAGCT 59.305 50.000 0.00 0.00 39.06 4.09
4052 4132 3.960102 GCCCCAATAGATCATTTCAACCA 59.040 43.478 0.00 0.00 0.00 3.67
4054 4134 5.302568 TCATGCCCCAATAGATCATTTCAAC 59.697 40.000 0.00 0.00 0.00 3.18
4056 4136 5.064314 TCATGCCCCAATAGATCATTTCA 57.936 39.130 0.00 0.00 0.00 2.69
4063 4143 2.092753 CGCCTATCATGCCCCAATAGAT 60.093 50.000 1.00 0.00 0.00 1.98
4067 4147 0.538057 CACGCCTATCATGCCCCAAT 60.538 55.000 0.00 0.00 0.00 3.16
4148 5916 8.824756 TCTTACGATAATCTAGGGCTCATAAT 57.175 34.615 0.00 0.00 0.00 1.28
4149 5917 8.824756 ATCTTACGATAATCTAGGGCTCATAA 57.175 34.615 0.00 0.00 0.00 1.90
4150 5918 8.824756 AATCTTACGATAATCTAGGGCTCATA 57.175 34.615 0.00 0.00 0.00 2.15
4151 5919 7.726033 AATCTTACGATAATCTAGGGCTCAT 57.274 36.000 0.00 0.00 0.00 2.90
4152 5920 7.148052 GCTAATCTTACGATAATCTAGGGCTCA 60.148 40.741 0.00 0.00 0.00 4.26
4153 5921 7.197703 GCTAATCTTACGATAATCTAGGGCTC 58.802 42.308 0.00 0.00 0.00 4.70
4154 5922 6.183360 CGCTAATCTTACGATAATCTAGGGCT 60.183 42.308 0.00 0.00 0.00 5.19
4155 5923 5.972382 CGCTAATCTTACGATAATCTAGGGC 59.028 44.000 0.00 0.00 0.00 5.19
4156 5924 7.317842 TCGCTAATCTTACGATAATCTAGGG 57.682 40.000 0.00 0.00 0.00 3.53
4237 6005 6.565234 ACTAGTGCAGCAAGTATTACTACTG 58.435 40.000 16.80 16.80 38.23 2.74
4244 6012 9.319143 CTAATCTAAACTAGTGCAGCAAGTATT 57.681 33.333 0.00 0.00 0.00 1.89
4246 6014 8.063200 TCTAATCTAAACTAGTGCAGCAAGTA 57.937 34.615 0.00 0.00 0.00 2.24
4247 6015 6.936279 TCTAATCTAAACTAGTGCAGCAAGT 58.064 36.000 0.00 0.00 0.00 3.16
4248 6016 6.478344 CCTCTAATCTAAACTAGTGCAGCAAG 59.522 42.308 0.00 0.00 0.00 4.01
4249 6017 6.154534 TCCTCTAATCTAAACTAGTGCAGCAA 59.845 38.462 0.00 0.00 0.00 3.91
4250 6018 5.656859 TCCTCTAATCTAAACTAGTGCAGCA 59.343 40.000 0.00 0.00 0.00 4.41
4251 6019 5.980715 GTCCTCTAATCTAAACTAGTGCAGC 59.019 44.000 0.00 0.00 0.00 5.25
4252 6020 7.101652 TGTCCTCTAATCTAAACTAGTGCAG 57.898 40.000 0.00 0.00 0.00 4.41
4253 6021 7.178628 ACTTGTCCTCTAATCTAAACTAGTGCA 59.821 37.037 0.00 0.00 0.00 4.57
4254 6022 7.489757 CACTTGTCCTCTAATCTAAACTAGTGC 59.510 40.741 0.00 0.00 35.13 4.40
4255 6023 7.976734 CCACTTGTCCTCTAATCTAAACTAGTG 59.023 40.741 0.00 0.00 38.95 2.74
4256 6024 7.674772 ACCACTTGTCCTCTAATCTAAACTAGT 59.325 37.037 0.00 0.00 0.00 2.57
4257 6025 7.976734 CACCACTTGTCCTCTAATCTAAACTAG 59.023 40.741 0.00 0.00 0.00 2.57
4258 6026 7.672660 TCACCACTTGTCCTCTAATCTAAACTA 59.327 37.037 0.00 0.00 0.00 2.24
4259 6027 6.497259 TCACCACTTGTCCTCTAATCTAAACT 59.503 38.462 0.00 0.00 0.00 2.66
4260 6028 6.698380 TCACCACTTGTCCTCTAATCTAAAC 58.302 40.000 0.00 0.00 0.00 2.01
4261 6029 6.497259 ACTCACCACTTGTCCTCTAATCTAAA 59.503 38.462 0.00 0.00 0.00 1.85
4262 6030 6.017192 ACTCACCACTTGTCCTCTAATCTAA 58.983 40.000 0.00 0.00 0.00 2.10
4263 6031 5.580998 ACTCACCACTTGTCCTCTAATCTA 58.419 41.667 0.00 0.00 0.00 1.98
4264 6032 4.421131 ACTCACCACTTGTCCTCTAATCT 58.579 43.478 0.00 0.00 0.00 2.40
4265 6033 4.810191 ACTCACCACTTGTCCTCTAATC 57.190 45.455 0.00 0.00 0.00 1.75
4266 6034 5.334421 ACTACTCACCACTTGTCCTCTAAT 58.666 41.667 0.00 0.00 0.00 1.73
4267 6035 4.737578 ACTACTCACCACTTGTCCTCTAA 58.262 43.478 0.00 0.00 0.00 2.10
4268 6036 4.383931 ACTACTCACCACTTGTCCTCTA 57.616 45.455 0.00 0.00 0.00 2.43
4269 6037 3.246416 ACTACTCACCACTTGTCCTCT 57.754 47.619 0.00 0.00 0.00 3.69
4270 6038 4.338379 AAACTACTCACCACTTGTCCTC 57.662 45.455 0.00 0.00 0.00 3.71
4271 6039 4.163458 TCAAAACTACTCACCACTTGTCCT 59.837 41.667 0.00 0.00 0.00 3.85
4272 6040 4.448210 TCAAAACTACTCACCACTTGTCC 58.552 43.478 0.00 0.00 0.00 4.02
4273 6041 6.619801 AATCAAAACTACTCACCACTTGTC 57.380 37.500 0.00 0.00 0.00 3.18
4274 6042 6.601613 TCAAATCAAAACTACTCACCACTTGT 59.398 34.615 0.00 0.00 0.00 3.16
4275 6043 7.026631 TCAAATCAAAACTACTCACCACTTG 57.973 36.000 0.00 0.00 0.00 3.16
4276 6044 7.285401 ACATCAAATCAAAACTACTCACCACTT 59.715 33.333 0.00 0.00 0.00 3.16
4277 6045 6.772716 ACATCAAATCAAAACTACTCACCACT 59.227 34.615 0.00 0.00 0.00 4.00
4278 6046 6.970484 ACATCAAATCAAAACTACTCACCAC 58.030 36.000 0.00 0.00 0.00 4.16
4290 6058 6.433716 TCATTCAGGTGCTACATCAAATCAAA 59.566 34.615 0.00 0.00 0.00 2.69
4318 6086 2.604912 TGGCTCCTTCAGACTGACTA 57.395 50.000 4.15 0.00 0.00 2.59
4324 6092 0.915364 ATCCCTTGGCTCCTTCAGAC 59.085 55.000 0.00 0.00 0.00 3.51
4446 6214 1.611673 CCAGGCTTGTTCATCGGAAGT 60.612 52.381 0.00 0.00 32.62 3.01
4447 6215 1.089920 CCAGGCTTGTTCATCGGAAG 58.910 55.000 0.00 0.00 32.62 3.46
4448 6216 0.322456 CCCAGGCTTGTTCATCGGAA 60.322 55.000 0.00 0.00 0.00 4.30
4466 6243 0.733909 GCACGCTGAAAAAGGATGCC 60.734 55.000 0.00 0.00 0.00 4.40
4617 6396 6.718454 TCATCTTCATGGCTTCTTCTCTTTTT 59.282 34.615 0.00 0.00 0.00 1.94
4618 6397 6.243900 TCATCTTCATGGCTTCTTCTCTTTT 58.756 36.000 0.00 0.00 0.00 2.27
4622 6401 5.007823 CACATCATCTTCATGGCTTCTTCTC 59.992 44.000 0.00 0.00 0.00 2.87
4684 6475 4.320567 GCTCTTCCCTCCTTTTTCTTTTCG 60.321 45.833 0.00 0.00 0.00 3.46
4700 6496 1.349357 AGTTCAGGGTTCAGCTCTTCC 59.651 52.381 0.00 0.00 0.00 3.46
4713 6509 2.926200 CTGCGTAAGTCATGAGTTCAGG 59.074 50.000 19.01 10.62 41.68 3.86
4746 6542 0.250252 TGCGCTCTTCATCACAACCA 60.250 50.000 9.73 0.00 0.00 3.67
4833 6629 0.843309 TCAAGAGGGGAACACAGCAA 59.157 50.000 0.00 0.00 0.00 3.91
4840 6636 3.879892 GTGAAGCATATCAAGAGGGGAAC 59.120 47.826 0.00 0.00 0.00 3.62
4901 6697 2.290323 ACTTACCACCACATCTCCTTGC 60.290 50.000 0.00 0.00 0.00 4.01
4995 6850 2.510948 GCAGTCGGCATATCAGTCG 58.489 57.895 0.00 0.00 43.97 4.18


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

AutoCloner maintained by Alex Coulton.