Multiple sequence alignment - TraesCS2B01G375100

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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 TraesCS2B01G375100 chr2B 100.000 2995 0 0 1 2995 536641267 536638273 0.000000e+00 5531.0
1 TraesCS2B01G375100 chr2A 91.069 2508 171 23 3 2469 595217590 595220085 0.000000e+00 3341.0
2 TraesCS2B01G375100 chr2A 91.852 270 15 4 2733 2995 595220221 595220490 1.310000e-98 370.0
3 TraesCS2B01G375100 chr2A 100.000 37 0 0 2677 2713 595220138 595220174 5.360000e-08 69.4
4 TraesCS2B01G375100 chr2D 92.679 1803 104 21 712 2495 455525158 455523365 0.000000e+00 2573.0
5 TraesCS2B01G375100 chr2D 90.365 685 52 7 3 680 455525836 455525159 0.000000e+00 887.0
6 TraesCS2B01G375100 chr2D 96.212 264 10 0 2732 2995 455523199 455522936 1.650000e-117 433.0
7 TraesCS2B01G375100 chr2D 85.385 260 20 11 2424 2673 455523812 455523561 1.380000e-63 254.0
8 TraesCS2B01G375100 chr2D 97.297 37 1 0 2677 2713 455523281 455523245 2.490000e-06 63.9
9 TraesCS2B01G375100 chr3D 85.950 121 16 1 1629 1748 333870660 333870780 8.710000e-26 128.0
10 TraesCS2B01G375100 chr1B 88.542 96 10 1 1654 1748 242189390 242189485 6.780000e-22 115.0
11 TraesCS2B01G375100 chr6D 84.783 92 14 0 1632 1723 158024635 158024726 3.180000e-15 93.5
12 TraesCS2B01G375100 chr6D 92.593 54 4 0 1670 1723 202136362 202136415 8.900000e-11 78.7
13 TraesCS2B01G375100 chr6B 84.783 92 14 0 1632 1723 285998440 285998531 3.180000e-15 93.5
14 TraesCS2B01G375100 chr5D 96.154 52 2 0 1675 1726 340787772 340787721 5.320000e-13 86.1
15 TraesCS2B01G375100 chr5B 92.593 54 4 0 1670 1723 402422895 402422948 8.900000e-11 78.7


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 TraesCS2B01G375100 chr2B 536638273 536641267 2994 True 5531.000000 5531 100.0000 1 2995 1 chr2B.!!$R1 2994
1 TraesCS2B01G375100 chr2A 595217590 595220490 2900 False 1260.133333 3341 94.3070 3 2995 3 chr2A.!!$F1 2992
2 TraesCS2B01G375100 chr2D 455522936 455525836 2900 True 842.180000 2573 92.3876 3 2995 5 chr2D.!!$R1 2992

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
641 651 0.040514 TTGTGTTTTGCGCGAGATGG 60.041 50.0 12.1 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2568 2611 0.036732 AGGCGAAAGATGGTGAAGCA 59.963 50.0 0.0 0.0 0.0 3.91 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
74 75 2.737252 GAGAGCCGAAGTGAATTTTCGT 59.263 45.455 9.28 0.00 44.30 3.85
79 80 6.009115 AGCCGAAGTGAATTTTCGTTTTAT 57.991 33.333 9.28 0.00 44.30 1.40
242 249 0.681564 AGACGAGGGAGTTGCTCGAT 60.682 55.000 0.00 0.00 42.46 3.59
243 250 0.173708 GACGAGGGAGTTGCTCGATT 59.826 55.000 0.00 0.00 42.46 3.34
244 251 0.173708 ACGAGGGAGTTGCTCGATTC 59.826 55.000 0.00 0.00 42.46 2.52
245 252 0.528684 CGAGGGAGTTGCTCGATTCC 60.529 60.000 0.00 0.00 42.46 3.01
272 279 0.474184 ATATAAAGGCCTGGCACGCT 59.526 50.000 22.05 5.48 0.00 5.07
379 386 4.777546 CATCCCACCCCTCCCCCA 62.778 72.222 0.00 0.00 0.00 4.96
380 387 4.455137 ATCCCACCCCTCCCCCAG 62.455 72.222 0.00 0.00 0.00 4.45
398 405 2.182791 CGACGTGCTCATGCTCCT 59.817 61.111 0.00 0.00 40.48 3.69
430 437 2.818274 GGTTAGCCGGCGTTGAGG 60.818 66.667 23.20 0.00 0.00 3.86
469 476 1.326951 TTGACGAGATGCCGGATCCA 61.327 55.000 13.41 0.00 0.00 3.41
471 478 2.029666 CGAGATGCCGGATCCACC 59.970 66.667 13.41 1.81 0.00 4.61
505 512 0.324368 TCCCGTGCATCTCCTGTAGT 60.324 55.000 0.00 0.00 0.00 2.73
509 516 1.474478 CGTGCATCTCCTGTAGTGTCT 59.526 52.381 0.00 0.00 0.00 3.41
529 536 1.154413 CGTCGTTGTTCATGGCAGC 60.154 57.895 0.00 0.00 0.00 5.25
534 541 0.316204 GTTGTTCATGGCAGCAGCTT 59.684 50.000 0.00 0.00 41.70 3.74
535 542 0.315886 TTGTTCATGGCAGCAGCTTG 59.684 50.000 0.00 0.00 41.70 4.01
544 551 0.936297 GCAGCAGCTTGTGTTTTCCG 60.936 55.000 0.00 0.00 37.91 4.30
556 563 3.119316 TGTGTTTTCCGCAGTGATTTGTT 60.119 39.130 0.00 0.00 0.00 2.83
558 565 3.380004 TGTTTTCCGCAGTGATTTGTTCT 59.620 39.130 0.00 0.00 0.00 3.01
563 570 2.416547 CCGCAGTGATTTGTTCTGTAGG 59.583 50.000 0.00 0.00 0.00 3.18
576 583 1.217183 TCTGTAGGCCGTCCTATTCCT 59.783 52.381 0.00 0.00 46.06 3.36
587 594 1.066605 TCCTATTCCTCGTTAGCGTGC 59.933 52.381 0.00 0.00 39.49 5.34
588 595 1.488527 CTATTCCTCGTTAGCGTGCC 58.511 55.000 0.00 0.00 39.49 5.01
597 604 1.517694 TTAGCGTGCCGATCCGTTC 60.518 57.895 0.00 0.00 0.00 3.95
600 607 2.807895 CGTGCCGATCCGTTCGTT 60.808 61.111 4.59 0.00 46.65 3.85
616 623 1.548719 TCGTTGTCCAGATGTGTAGGG 59.451 52.381 0.00 0.00 0.00 3.53
624 631 3.054434 TCCAGATGTGTAGGGGATGTTTG 60.054 47.826 0.00 0.00 0.00 2.93
641 651 0.040514 TTGTGTTTTGCGCGAGATGG 60.041 50.000 12.10 0.00 0.00 3.51
683 696 5.564651 CGTGAAATTAGATGCTTGTTTGGGT 60.565 40.000 0.00 0.00 0.00 4.51
693 706 2.549926 CTTGTTTGGGTTTGTGGCTTC 58.450 47.619 0.00 0.00 0.00 3.86
694 707 0.827368 TGTTTGGGTTTGTGGCTTCC 59.173 50.000 0.00 0.00 0.00 3.46
725 739 5.977635 TCCAGTTCATGACGAATGAGTTAT 58.022 37.500 0.00 0.00 46.01 1.89
751 765 5.289917 TCCGTTTATAGTTGTTGCATGTG 57.710 39.130 0.00 0.00 0.00 3.21
758 772 8.479280 GTTTATAGTTGTTGCATGTGTTTTCAG 58.521 33.333 0.00 0.00 0.00 3.02
792 806 1.927174 CGAAATACTGTGCTCGGGAAG 59.073 52.381 0.00 0.00 0.00 3.46
840 854 3.306364 CCTTGTGGTAGAAGACACTCTGG 60.306 52.174 0.00 0.00 38.39 3.86
855 869 1.280421 CTCTGGGTTGCTTTAGCTCCT 59.720 52.381 3.10 0.00 42.66 3.69
864 879 5.813157 GGTTGCTTTAGCTCCTAAACTAGAG 59.187 44.000 0.00 0.00 42.66 2.43
889 904 5.479306 AGTTTACTCTGCGAACACACATAT 58.521 37.500 0.00 0.00 0.00 1.78
904 919 9.846248 GAACACACATATCTTGCTTTTCTAATT 57.154 29.630 0.00 0.00 0.00 1.40
933 949 7.924412 TCGCTGTATTTTCCTATATCGTTTCTT 59.076 33.333 0.00 0.00 0.00 2.52
1049 1066 1.142870 GCAGAACTATGTGCCCCCATA 59.857 52.381 0.00 0.00 39.82 2.74
1050 1067 2.851195 CAGAACTATGTGCCCCCATAC 58.149 52.381 0.00 0.00 0.00 2.39
1056 1074 4.278310 ACTATGTGCCCCCATACTTTTTC 58.722 43.478 0.00 0.00 0.00 2.29
1060 1078 1.899142 TGCCCCCATACTTTTTCTTGC 59.101 47.619 0.00 0.00 0.00 4.01
1073 1091 5.993441 ACTTTTTCTTGCAAATGCTAATGCT 59.007 32.000 0.00 0.00 42.97 3.79
1094 1112 4.093556 GCTAACATGTCAGGTGCTTTAGAC 59.906 45.833 0.00 0.00 0.00 2.59
1103 1122 2.441750 AGGTGCTTTAGACTTGGGTCAA 59.558 45.455 0.00 0.00 44.36 3.18
1117 1136 3.211045 TGGGTCAAGTGTAGTTCAAAGC 58.789 45.455 0.00 0.00 0.00 3.51
1181 1200 5.306532 AGTCAACATGATTGAATGCAGTC 57.693 39.130 7.33 7.33 0.00 3.51
1186 1205 5.562506 ACATGATTGAATGCAGTCTTCAG 57.437 39.130 16.05 13.04 34.33 3.02
1298 1322 5.945784 TCCAATAGTATGCTCTGCAAGTTTT 59.054 36.000 0.00 0.00 43.62 2.43
1424 1451 2.169832 TGTCTTGCTGCTAAGTCCAC 57.830 50.000 0.00 0.00 0.00 4.02
1630 1657 2.693864 AGGATCAGCACCCCTGGG 60.694 66.667 5.50 5.50 42.05 4.45
1640 1667 2.356667 CCCCTGGGAGGAACAAGC 59.643 66.667 16.20 0.00 37.67 4.01
1642 1669 1.301293 CCCTGGGAGGAACAAGCTC 59.699 63.158 7.01 0.00 37.67 4.09
1645 1672 0.539051 CTGGGAGGAACAAGCTCGAT 59.461 55.000 0.00 0.00 0.00 3.59
1648 1675 1.066143 GGGAGGAACAAGCTCGATCAA 60.066 52.381 0.00 0.00 0.00 2.57
1651 1678 4.503991 GGGAGGAACAAGCTCGATCAATAT 60.504 45.833 0.00 0.00 0.00 1.28
1687 1714 0.038251 CGCTTACCACTGAGTCTGCA 60.038 55.000 0.00 0.00 0.00 4.41
1699 1726 5.063691 CACTGAGTCTGCAATGAAGAAGATC 59.936 44.000 0.00 0.00 0.00 2.75
1702 1729 4.431809 AGTCTGCAATGAAGAAGATCGAG 58.568 43.478 0.00 0.00 0.00 4.04
1714 1741 3.069586 AGAAGATCGAGGACAACAACACA 59.930 43.478 0.00 0.00 0.00 3.72
1717 1744 2.218953 TCGAGGACAACAACACACTC 57.781 50.000 0.00 0.00 0.00 3.51
1756 1783 3.244561 TGAAGGCCGACAAGAAGAAGATT 60.245 43.478 0.00 0.00 0.00 2.40
1762 1789 3.623510 CCGACAAGAAGAAGATTAAGGCC 59.376 47.826 0.00 0.00 0.00 5.19
1967 1994 3.027412 ACCAGACTACGATGCTCTTGAT 58.973 45.455 0.00 0.00 0.00 2.57
2082 2109 2.007608 GTTACTTAGCAAAGGGGCTCG 58.992 52.381 0.00 0.00 44.54 5.03
2218 2247 6.442541 TCTTTACCATCCTTTGACTTACCA 57.557 37.500 0.00 0.00 0.00 3.25
2294 2323 0.392193 CTGCTTTGGGCGATGAGACT 60.392 55.000 0.00 0.00 45.43 3.24
2298 2329 0.396435 TTTGGGCGATGAGACTGTGT 59.604 50.000 0.00 0.00 0.00 3.72
2299 2330 0.320683 TTGGGCGATGAGACTGTGTG 60.321 55.000 0.00 0.00 0.00 3.82
2300 2331 2.103042 GGGCGATGAGACTGTGTGC 61.103 63.158 0.00 0.00 0.00 4.57
2301 2332 2.103042 GGCGATGAGACTGTGTGCC 61.103 63.158 0.00 0.00 0.00 5.01
2302 2333 2.447887 GCGATGAGACTGTGTGCCG 61.448 63.158 0.00 0.00 0.00 5.69
2387 2429 3.004734 GCATGTTGATGGTTAGGCATACC 59.995 47.826 0.00 1.46 36.17 2.73
2404 2446 1.734163 ACCTATGCACAGTTAACGGC 58.266 50.000 5.60 9.01 0.00 5.68
2407 2449 0.325272 TATGCACAGTTAACGGCCCA 59.675 50.000 14.47 8.75 0.00 5.36
2408 2450 0.960364 ATGCACAGTTAACGGCCCAG 60.960 55.000 14.47 0.00 0.00 4.45
2413 2455 0.887933 CAGTTAACGGCCCAGCAATT 59.112 50.000 0.00 0.00 0.00 2.32
2433 2475 8.190784 AGCAATTATCAGCTGTAATTTTGTACC 58.809 33.333 21.51 11.82 40.13 3.34
2434 2476 7.435192 GCAATTATCAGCTGTAATTTTGTACCC 59.565 37.037 21.51 6.70 31.28 3.69
2495 2538 2.162319 TCGCTGCACACTTTCATGTA 57.838 45.000 0.00 0.00 0.00 2.29
2496 2539 2.698803 TCGCTGCACACTTTCATGTAT 58.301 42.857 0.00 0.00 0.00 2.29
2497 2540 3.073678 TCGCTGCACACTTTCATGTATT 58.926 40.909 0.00 0.00 0.00 1.89
2498 2541 3.501828 TCGCTGCACACTTTCATGTATTT 59.498 39.130 0.00 0.00 0.00 1.40
2499 2542 3.605056 CGCTGCACACTTTCATGTATTTG 59.395 43.478 0.00 0.00 0.00 2.32
2500 2543 4.613394 CGCTGCACACTTTCATGTATTTGA 60.613 41.667 0.00 0.00 0.00 2.69
2501 2544 5.404946 GCTGCACACTTTCATGTATTTGAT 58.595 37.500 0.00 0.00 0.00 2.57
2502 2545 5.287752 GCTGCACACTTTCATGTATTTGATG 59.712 40.000 0.00 0.00 0.00 3.07
2503 2546 5.162794 TGCACACTTTCATGTATTTGATGC 58.837 37.500 0.00 0.00 30.80 3.91
2504 2547 5.162794 GCACACTTTCATGTATTTGATGCA 58.837 37.500 0.00 0.00 30.62 3.96
2505 2548 5.634439 GCACACTTTCATGTATTTGATGCAA 59.366 36.000 0.00 0.00 30.62 4.08
2506 2549 6.400303 GCACACTTTCATGTATTTGATGCAAC 60.400 38.462 0.00 0.00 30.62 4.17
2507 2550 5.858049 ACACTTTCATGTATTTGATGCAACG 59.142 36.000 0.00 0.00 0.00 4.10
2508 2551 6.085573 CACTTTCATGTATTTGATGCAACGA 58.914 36.000 0.00 0.00 0.00 3.85
2509 2552 6.748658 CACTTTCATGTATTTGATGCAACGAT 59.251 34.615 0.00 0.00 0.00 3.73
2510 2553 6.968904 ACTTTCATGTATTTGATGCAACGATC 59.031 34.615 0.00 0.00 0.00 3.69
2511 2554 5.422666 TCATGTATTTGATGCAACGATCC 57.577 39.130 0.00 0.00 0.00 3.36
2512 2555 4.880696 TCATGTATTTGATGCAACGATCCA 59.119 37.500 0.00 0.00 0.00 3.41
2513 2556 5.356470 TCATGTATTTGATGCAACGATCCAA 59.644 36.000 0.00 0.00 0.00 3.53
2514 2557 5.233957 TGTATTTGATGCAACGATCCAAG 57.766 39.130 0.00 0.00 0.00 3.61
2515 2558 4.699735 TGTATTTGATGCAACGATCCAAGT 59.300 37.500 0.00 0.00 0.00 3.16
2516 2559 3.557577 TTTGATGCAACGATCCAAGTG 57.442 42.857 0.00 0.00 0.00 3.16
2517 2560 2.470983 TGATGCAACGATCCAAGTGA 57.529 45.000 0.00 0.00 0.00 3.41
2518 2561 2.076100 TGATGCAACGATCCAAGTGAC 58.924 47.619 0.00 0.00 0.00 3.67
2519 2562 1.398390 GATGCAACGATCCAAGTGACC 59.602 52.381 0.00 0.00 0.00 4.02
2520 2563 0.605319 TGCAACGATCCAAGTGACCC 60.605 55.000 0.00 0.00 0.00 4.46
2521 2564 1.635663 GCAACGATCCAAGTGACCCG 61.636 60.000 0.00 0.00 0.00 5.28
2522 2565 0.320421 CAACGATCCAAGTGACCCGT 60.320 55.000 0.00 0.00 37.25 5.28
2523 2566 0.320421 AACGATCCAAGTGACCCGTG 60.320 55.000 0.00 0.00 36.25 4.94
2524 2567 1.292223 CGATCCAAGTGACCCGTGT 59.708 57.895 0.00 0.00 0.00 4.49
2525 2568 0.320421 CGATCCAAGTGACCCGTGTT 60.320 55.000 0.00 0.00 0.00 3.32
2526 2569 1.156736 GATCCAAGTGACCCGTGTTG 58.843 55.000 0.00 0.00 0.00 3.33
2527 2570 0.889186 ATCCAAGTGACCCGTGTTGC 60.889 55.000 0.00 0.00 0.00 4.17
2528 2571 1.525995 CCAAGTGACCCGTGTTGCT 60.526 57.895 0.00 0.00 0.00 3.91
2529 2572 0.250124 CCAAGTGACCCGTGTTGCTA 60.250 55.000 0.00 0.00 0.00 3.49
2530 2573 1.588674 CAAGTGACCCGTGTTGCTAA 58.411 50.000 0.00 0.00 0.00 3.09
2531 2574 1.944024 CAAGTGACCCGTGTTGCTAAA 59.056 47.619 0.00 0.00 0.00 1.85
2532 2575 2.552315 CAAGTGACCCGTGTTGCTAAAT 59.448 45.455 0.00 0.00 0.00 1.40
2533 2576 2.423577 AGTGACCCGTGTTGCTAAATC 58.576 47.619 0.00 0.00 0.00 2.17
2534 2577 1.127951 GTGACCCGTGTTGCTAAATCG 59.872 52.381 0.00 0.00 0.00 3.34
2535 2578 1.001068 TGACCCGTGTTGCTAAATCGA 59.999 47.619 0.00 0.00 0.00 3.59
2536 2579 1.659098 GACCCGTGTTGCTAAATCGAG 59.341 52.381 0.00 0.00 0.00 4.04
2537 2580 0.373716 CCCGTGTTGCTAAATCGAGC 59.626 55.000 0.00 0.00 43.16 5.03
2538 2581 1.359848 CCGTGTTGCTAAATCGAGCT 58.640 50.000 0.00 0.00 43.27 4.09
2539 2582 1.732259 CCGTGTTGCTAAATCGAGCTT 59.268 47.619 0.00 0.00 43.27 3.74
2540 2583 2.159627 CCGTGTTGCTAAATCGAGCTTT 59.840 45.455 0.00 0.00 43.27 3.51
2541 2584 3.155998 CGTGTTGCTAAATCGAGCTTTG 58.844 45.455 0.00 0.00 43.27 2.77
2542 2585 2.911102 GTGTTGCTAAATCGAGCTTTGC 59.089 45.455 8.76 8.76 43.27 3.68
2543 2586 2.169179 GTTGCTAAATCGAGCTTTGCG 58.831 47.619 10.34 0.00 43.27 4.85
2544 2587 1.438651 TGCTAAATCGAGCTTTGCGT 58.561 45.000 10.34 0.00 43.27 5.24
2545 2588 1.804151 TGCTAAATCGAGCTTTGCGTT 59.196 42.857 10.34 0.00 43.27 4.84
2546 2589 2.225491 TGCTAAATCGAGCTTTGCGTTT 59.775 40.909 10.34 0.00 43.27 3.60
2547 2590 2.589841 GCTAAATCGAGCTTTGCGTTTG 59.410 45.455 0.00 0.00 39.50 2.93
2548 2591 2.050477 AAATCGAGCTTTGCGTTTGG 57.950 45.000 0.00 0.00 0.00 3.28
2549 2592 0.951558 AATCGAGCTTTGCGTTTGGT 59.048 45.000 0.00 0.00 0.00 3.67
2550 2593 0.517316 ATCGAGCTTTGCGTTTGGTC 59.483 50.000 0.00 0.00 0.00 4.02
2551 2594 0.531974 TCGAGCTTTGCGTTTGGTCT 60.532 50.000 0.00 0.00 0.00 3.85
2552 2595 0.307760 CGAGCTTTGCGTTTGGTCTT 59.692 50.000 0.00 0.00 0.00 3.01
2553 2596 1.529438 CGAGCTTTGCGTTTGGTCTTA 59.471 47.619 0.00 0.00 0.00 2.10
2554 2597 2.661979 CGAGCTTTGCGTTTGGTCTTAC 60.662 50.000 0.00 0.00 0.00 2.34
2555 2598 1.607148 AGCTTTGCGTTTGGTCTTACC 59.393 47.619 0.00 0.00 39.22 2.85
2575 2618 3.848726 CCATATTGGTTGGTTGCTTCAC 58.151 45.455 0.00 0.00 31.35 3.18
2576 2619 3.368323 CCATATTGGTTGGTTGCTTCACC 60.368 47.826 0.00 0.00 33.02 4.02
2577 2620 1.786937 ATTGGTTGGTTGCTTCACCA 58.213 45.000 0.00 0.00 45.68 4.17
2578 2621 1.786937 TTGGTTGGTTGCTTCACCAT 58.213 45.000 4.12 0.00 46.60 3.55
2579 2622 1.327303 TGGTTGGTTGCTTCACCATC 58.673 50.000 4.12 3.98 46.60 3.51
2580 2623 1.133513 TGGTTGGTTGCTTCACCATCT 60.134 47.619 4.12 0.00 46.60 2.90
2581 2624 1.963515 GGTTGGTTGCTTCACCATCTT 59.036 47.619 4.12 0.00 46.60 2.40
2582 2625 2.365293 GGTTGGTTGCTTCACCATCTTT 59.635 45.455 4.12 0.00 46.60 2.52
2583 2626 3.552890 GGTTGGTTGCTTCACCATCTTTC 60.553 47.826 4.12 0.00 46.60 2.62
2584 2627 1.879380 TGGTTGCTTCACCATCTTTCG 59.121 47.619 0.00 0.00 42.27 3.46
2585 2628 1.401539 GGTTGCTTCACCATCTTTCGC 60.402 52.381 0.00 0.00 36.73 4.70
2586 2629 0.881118 TTGCTTCACCATCTTTCGCC 59.119 50.000 0.00 0.00 0.00 5.54
2587 2630 0.036732 TGCTTCACCATCTTTCGCCT 59.963 50.000 0.00 0.00 0.00 5.52
2588 2631 0.729690 GCTTCACCATCTTTCGCCTC 59.270 55.000 0.00 0.00 0.00 4.70
2589 2632 1.002366 CTTCACCATCTTTCGCCTCG 58.998 55.000 0.00 0.00 0.00 4.63
2590 2633 0.320374 TTCACCATCTTTCGCCTCGT 59.680 50.000 0.00 0.00 0.00 4.18
2591 2634 0.108804 TCACCATCTTTCGCCTCGTC 60.109 55.000 0.00 0.00 0.00 4.20
2592 2635 0.389817 CACCATCTTTCGCCTCGTCA 60.390 55.000 0.00 0.00 0.00 4.35
2593 2636 0.537188 ACCATCTTTCGCCTCGTCAT 59.463 50.000 0.00 0.00 0.00 3.06
2594 2637 1.754803 ACCATCTTTCGCCTCGTCATA 59.245 47.619 0.00 0.00 0.00 2.15
2595 2638 2.365617 ACCATCTTTCGCCTCGTCATAT 59.634 45.455 0.00 0.00 0.00 1.78
2596 2639 2.989840 CCATCTTTCGCCTCGTCATATC 59.010 50.000 0.00 0.00 0.00 1.63
2597 2640 3.305676 CCATCTTTCGCCTCGTCATATCT 60.306 47.826 0.00 0.00 0.00 1.98
2598 2641 3.627732 TCTTTCGCCTCGTCATATCTC 57.372 47.619 0.00 0.00 0.00 2.75
2599 2642 2.293677 TCTTTCGCCTCGTCATATCTCC 59.706 50.000 0.00 0.00 0.00 3.71
2600 2643 1.982660 TTCGCCTCGTCATATCTCCT 58.017 50.000 0.00 0.00 0.00 3.69
2601 2644 1.239347 TCGCCTCGTCATATCTCCTG 58.761 55.000 0.00 0.00 0.00 3.86
2602 2645 0.955178 CGCCTCGTCATATCTCCTGT 59.045 55.000 0.00 0.00 0.00 4.00
2603 2646 2.152016 CGCCTCGTCATATCTCCTGTA 58.848 52.381 0.00 0.00 0.00 2.74
2604 2647 2.750166 CGCCTCGTCATATCTCCTGTAT 59.250 50.000 0.00 0.00 0.00 2.29
2605 2648 3.939592 CGCCTCGTCATATCTCCTGTATA 59.060 47.826 0.00 0.00 0.00 1.47
2606 2649 4.395231 CGCCTCGTCATATCTCCTGTATAA 59.605 45.833 0.00 0.00 0.00 0.98
2607 2650 5.066634 CGCCTCGTCATATCTCCTGTATAAT 59.933 44.000 0.00 0.00 0.00 1.28
2608 2651 6.404844 CGCCTCGTCATATCTCCTGTATAATT 60.405 42.308 0.00 0.00 0.00 1.40
2609 2652 7.324178 GCCTCGTCATATCTCCTGTATAATTT 58.676 38.462 0.00 0.00 0.00 1.82
2610 2653 7.489757 GCCTCGTCATATCTCCTGTATAATTTC 59.510 40.741 0.00 0.00 0.00 2.17
2611 2654 7.976734 CCTCGTCATATCTCCTGTATAATTTCC 59.023 40.741 0.00 0.00 0.00 3.13
2612 2655 8.651589 TCGTCATATCTCCTGTATAATTTCCT 57.348 34.615 0.00 0.00 0.00 3.36
2613 2656 8.523658 TCGTCATATCTCCTGTATAATTTCCTG 58.476 37.037 0.00 0.00 0.00 3.86
2614 2657 8.523658 CGTCATATCTCCTGTATAATTTCCTGA 58.476 37.037 0.00 0.00 0.00 3.86
2619 2662 8.915057 ATCTCCTGTATAATTTCCTGATTGTG 57.085 34.615 0.00 0.00 0.00 3.33
2620 2663 6.767902 TCTCCTGTATAATTTCCTGATTGTGC 59.232 38.462 0.00 0.00 0.00 4.57
2621 2664 6.662755 TCCTGTATAATTTCCTGATTGTGCT 58.337 36.000 0.00 0.00 0.00 4.40
2622 2665 7.118723 TCCTGTATAATTTCCTGATTGTGCTT 58.881 34.615 0.00 0.00 0.00 3.91
2623 2666 7.067372 TCCTGTATAATTTCCTGATTGTGCTTG 59.933 37.037 0.00 0.00 0.00 4.01
2624 2667 7.148018 CCTGTATAATTTCCTGATTGTGCTTGT 60.148 37.037 0.00 0.00 0.00 3.16
2639 2682 2.258755 GCTTGTTGTGTGTTTGTGGTC 58.741 47.619 0.00 0.00 0.00 4.02
2640 2683 2.094752 GCTTGTTGTGTGTTTGTGGTCT 60.095 45.455 0.00 0.00 0.00 3.85
2641 2684 3.613910 GCTTGTTGTGTGTTTGTGGTCTT 60.614 43.478 0.00 0.00 0.00 3.01
2653 2696 1.032014 GTGGTCTTTGCTGCTTTGGA 58.968 50.000 0.00 0.00 0.00 3.53
2673 2716 0.733150 CGATGAGACAGAGTGCCGTA 59.267 55.000 0.00 0.00 0.00 4.02
2674 2717 1.268285 CGATGAGACAGAGTGCCGTAG 60.268 57.143 0.00 0.00 0.00 3.51
2675 2718 0.457851 ATGAGACAGAGTGCCGTAGC 59.542 55.000 0.00 0.00 40.48 3.58
2723 2800 8.375493 TGAAACTATCAGGTTAACTATCAGGT 57.625 34.615 5.42 0.00 33.04 4.00
2725 2802 9.099454 GAAACTATCAGGTTAACTATCAGGTTG 57.901 37.037 5.42 0.00 0.00 3.77
2727 2804 8.554490 ACTATCAGGTTAACTATCAGGTTGAT 57.446 34.615 5.42 5.47 40.72 2.57
2728 2805 8.424918 ACTATCAGGTTAACTATCAGGTTGATG 58.575 37.037 5.42 0.00 37.70 3.07
2729 2806 6.867519 TCAGGTTAACTATCAGGTTGATGA 57.132 37.500 5.42 0.00 37.70 2.92
2730 2807 7.437713 TCAGGTTAACTATCAGGTTGATGAT 57.562 36.000 5.42 0.00 42.52 2.45
2775 2879 6.526566 AAAACTAAGAATCGGCGATGTATC 57.473 37.500 24.73 17.10 0.00 2.24
2777 2881 4.547532 ACTAAGAATCGGCGATGTATCAC 58.452 43.478 24.73 10.59 0.00 3.06
2778 2882 3.452755 AAGAATCGGCGATGTATCACA 57.547 42.857 24.73 0.00 0.00 3.58
2779 2883 3.452755 AGAATCGGCGATGTATCACAA 57.547 42.857 24.73 0.00 0.00 3.33
2780 2884 3.384668 AGAATCGGCGATGTATCACAAG 58.615 45.455 24.73 0.00 0.00 3.16
2826 2937 5.179368 CGAGCAACCAAGTCAAATTAGAGAA 59.821 40.000 0.00 0.00 0.00 2.87
2827 2938 6.128172 CGAGCAACCAAGTCAAATTAGAGAAT 60.128 38.462 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.741476 CCGCTCCTGCTGCCAAAC 61.741 66.667 0.00 0.00 36.97 2.93
79 80 8.390854 TCTCGTTTTAAATTGTTTTGCGTTTA 57.609 26.923 0.00 0.00 0.00 2.01
176 183 2.815647 GCTGTACAGAGCACCGCC 60.816 66.667 27.08 1.99 38.95 6.13
235 242 1.043116 ATCGTGGAGGGAATCGAGCA 61.043 55.000 0.00 0.00 35.85 4.26
242 249 2.370849 GGCCTTTATATCGTGGAGGGAA 59.629 50.000 0.00 0.00 0.00 3.97
243 250 1.975680 GGCCTTTATATCGTGGAGGGA 59.024 52.381 0.00 0.00 0.00 4.20
244 251 1.978580 AGGCCTTTATATCGTGGAGGG 59.021 52.381 0.00 0.00 0.00 4.30
245 252 2.289694 CCAGGCCTTTATATCGTGGAGG 60.290 54.545 0.00 0.00 37.82 4.30
272 279 2.609610 AGGAACCCTAGCGGCCAA 60.610 61.111 2.24 0.00 33.26 4.52
380 387 3.558411 GGAGCATGAGCACGTCGC 61.558 66.667 0.00 2.28 45.49 5.19
383 390 0.969917 AGAGAGGAGCATGAGCACGT 60.970 55.000 0.00 0.00 45.49 4.49
398 405 1.743958 CTAACCGAGGCGAAGAAGAGA 59.256 52.381 0.00 0.00 0.00 3.10
471 478 4.612536 GGATTTCGCGCGCATGGG 62.613 66.667 32.61 15.11 0.00 4.00
494 501 1.746220 GACGCAGACACTACAGGAGAT 59.254 52.381 0.00 0.00 0.00 2.75
505 512 0.858583 CATGAACAACGACGCAGACA 59.141 50.000 0.00 0.00 0.00 3.41
509 516 1.840630 CTGCCATGAACAACGACGCA 61.841 55.000 0.00 0.00 0.00 5.24
529 536 0.381801 ACTGCGGAAAACACAAGCTG 59.618 50.000 0.00 0.00 0.00 4.24
534 541 2.425312 ACAAATCACTGCGGAAAACACA 59.575 40.909 0.00 0.00 0.00 3.72
535 542 3.078594 ACAAATCACTGCGGAAAACAC 57.921 42.857 0.00 0.00 0.00 3.32
544 551 2.162408 GGCCTACAGAACAAATCACTGC 59.838 50.000 0.00 0.00 35.38 4.40
563 570 1.602416 GCTAACGAGGAATAGGACGGC 60.602 57.143 0.00 0.00 0.00 5.68
597 604 1.405526 CCCCTACACATCTGGACAACG 60.406 57.143 0.00 0.00 0.00 4.10
600 607 2.118679 CATCCCCTACACATCTGGACA 58.881 52.381 0.00 0.00 0.00 4.02
616 623 0.502275 CGCGCAAAACACAAACATCC 59.498 50.000 8.75 0.00 0.00 3.51
624 631 0.452784 GACCATCTCGCGCAAAACAC 60.453 55.000 8.75 0.00 0.00 3.32
641 651 1.666209 CGCCCAAATCCACCCATGAC 61.666 60.000 0.00 0.00 0.00 3.06
683 696 0.031616 AAACAGGGGGAAGCCACAAA 60.032 50.000 0.00 0.00 0.00 2.83
725 739 5.752892 TGCAACAACTATAAACGGAACAA 57.247 34.783 0.00 0.00 0.00 2.83
751 765 2.872858 GACAGACCCTGTGACTGAAAAC 59.127 50.000 4.14 0.00 45.44 2.43
758 772 2.457366 ATTTCGACAGACCCTGTGAC 57.543 50.000 4.14 0.00 45.44 3.67
792 806 6.582437 AAATCGAAATCCAAACAACAACAC 57.418 33.333 0.00 0.00 0.00 3.32
834 848 1.003696 GGAGCTAAAGCAACCCAGAGT 59.996 52.381 4.54 0.00 45.16 3.24
840 854 5.731591 TCTAGTTTAGGAGCTAAAGCAACC 58.268 41.667 4.54 7.34 45.16 3.77
864 879 4.046462 TGTGTGTTCGCAGAGTAAACTAC 58.954 43.478 0.00 0.00 38.43 2.73
871 886 3.876274 AGATATGTGTGTTCGCAGAGT 57.124 42.857 0.00 0.00 38.43 3.24
889 904 6.503524 ACAGCGAAAAATTAGAAAAGCAAGA 58.496 32.000 0.00 0.00 0.00 3.02
904 919 8.428186 AACGATATAGGAAAATACAGCGAAAA 57.572 30.769 0.00 0.00 0.00 2.29
905 920 8.428186 AAACGATATAGGAAAATACAGCGAAA 57.572 30.769 0.00 0.00 0.00 3.46
906 921 7.924412 AGAAACGATATAGGAAAATACAGCGAA 59.076 33.333 0.00 0.00 0.00 4.70
909 924 8.827677 ACAAGAAACGATATAGGAAAATACAGC 58.172 33.333 0.00 0.00 0.00 4.40
933 949 7.436933 AGCAGTGATTTCAGATCGATATAACA 58.563 34.615 0.00 0.00 0.00 2.41
1049 1066 5.993441 AGCATTAGCATTTGCAAGAAAAAGT 59.007 32.000 5.20 0.00 45.49 2.66
1050 1067 6.476243 AGCATTAGCATTTGCAAGAAAAAG 57.524 33.333 5.20 0.00 45.49 2.27
1056 1074 5.808540 ACATGTTAGCATTAGCATTTGCAAG 59.191 36.000 5.20 0.00 45.49 4.01
1060 1078 5.975344 CCTGACATGTTAGCATTAGCATTTG 59.025 40.000 12.02 0.00 45.49 2.32
1073 1091 5.483685 AGTCTAAAGCACCTGACATGTTA 57.516 39.130 0.00 0.00 32.41 2.41
1094 1112 4.261197 GCTTTGAACTACACTTGACCCAAG 60.261 45.833 5.26 5.26 45.85 3.61
1103 1122 5.588648 TGTAAAGCAAGCTTTGAACTACACT 59.411 36.000 25.64 2.48 44.84 3.55
1117 1136 6.902341 ACAATACTGTGACATGTAAAGCAAG 58.098 36.000 0.00 0.00 33.30 4.01
1146 1165 8.896744 CAATCATGTTGACTAATCCAATAGTGT 58.103 33.333 0.00 0.00 36.28 3.55
1159 1178 5.008331 AGACTGCATTCAATCATGTTGACT 58.992 37.500 6.84 3.63 0.00 3.41
1181 1200 9.965824 ACATTTTACAAGAACCAAATACTGAAG 57.034 29.630 0.00 0.00 0.00 3.02
1298 1322 6.406370 AGTAACAAGTTGCAGCATATCACTA 58.594 36.000 2.55 0.00 0.00 2.74
1630 1657 5.292765 TGATATTGATCGAGCTTGTTCCTC 58.707 41.667 0.90 3.07 34.49 3.71
1640 1667 6.923012 ACTTGAGGATCTGATATTGATCGAG 58.077 40.000 11.18 0.00 40.71 4.04
1642 1669 7.032580 GGTACTTGAGGATCTGATATTGATCG 58.967 42.308 11.18 0.00 40.71 3.69
1645 1672 5.243954 CGGGTACTTGAGGATCTGATATTGA 59.756 44.000 0.00 0.00 34.92 2.57
1648 1675 3.511934 GCGGGTACTTGAGGATCTGATAT 59.488 47.826 0.00 0.00 34.92 1.63
1651 1678 1.112113 GCGGGTACTTGAGGATCTGA 58.888 55.000 0.00 0.00 34.92 3.27
1687 1714 5.152623 TGTTGTCCTCGATCTTCTTCATT 57.847 39.130 0.00 0.00 0.00 2.57
1699 1726 0.852777 CGAGTGTGTTGTTGTCCTCG 59.147 55.000 0.00 0.00 36.31 4.63
1702 1729 1.935933 AGACGAGTGTGTTGTTGTCC 58.064 50.000 0.00 0.00 0.00 4.02
1714 1741 0.447011 GGTCGACGATGAAGACGAGT 59.553 55.000 9.92 0.00 38.73 4.18
1717 1744 0.446616 TCAGGTCGACGATGAAGACG 59.553 55.000 16.95 0.00 35.87 4.18
1756 1783 2.264005 TTTTCTTGACAGCGGCCTTA 57.736 45.000 0.00 0.00 0.00 2.69
1762 1789 3.183574 TGTCGTACATTTTCTTGACAGCG 59.816 43.478 0.00 0.00 32.96 5.18
1967 1994 4.395519 CCGATCTTGTTGGCCACA 57.604 55.556 3.88 4.06 0.00 4.17
2218 2247 9.429109 AAAACCGGGAAATTATACAGGAAATAT 57.571 29.630 6.32 0.00 0.00 1.28
2294 2323 1.745653 TCAATCACAAAACGGCACACA 59.254 42.857 0.00 0.00 0.00 3.72
2298 2329 1.336440 CCAGTCAATCACAAAACGGCA 59.664 47.619 0.00 0.00 0.00 5.69
2299 2330 1.336755 ACCAGTCAATCACAAAACGGC 59.663 47.619 0.00 0.00 0.00 5.68
2300 2331 3.371168 CAACCAGTCAATCACAAAACGG 58.629 45.455 0.00 0.00 0.00 4.44
2301 2332 2.788786 GCAACCAGTCAATCACAAAACG 59.211 45.455 0.00 0.00 0.00 3.60
2302 2333 3.779759 TGCAACCAGTCAATCACAAAAC 58.220 40.909 0.00 0.00 0.00 2.43
2345 2387 6.779049 ACATGCCATGTAATTTCAGATACCAT 59.221 34.615 8.96 0.00 42.78 3.55
2387 2429 1.014352 GGGCCGTTAACTGTGCATAG 58.986 55.000 9.17 9.17 0.00 2.23
2402 2444 3.122369 AGCTGATAATTGCTGGGCC 57.878 52.632 0.00 0.00 38.21 5.80
2407 2449 8.190784 GGTACAAAATTACAGCTGATAATTGCT 58.809 33.333 23.35 13.42 40.54 3.91
2408 2450 7.435192 GGGTACAAAATTACAGCTGATAATTGC 59.565 37.037 23.35 13.11 33.51 3.56
2413 2455 8.545472 AGTAAGGGTACAAAATTACAGCTGATA 58.455 33.333 23.35 7.93 31.90 2.15
2433 2475 2.026262 TGAGGCCCTTTGCTAAGTAAGG 60.026 50.000 0.00 2.68 40.50 2.69
2434 2476 3.274288 CTGAGGCCCTTTGCTAAGTAAG 58.726 50.000 0.00 0.00 40.92 2.34
2471 2514 1.398041 TGAAAGTGTGCAGCGATATGC 59.602 47.619 0.00 0.00 46.68 3.14
2486 2529 6.415867 GGATCGTTGCATCAAATACATGAAAG 59.584 38.462 0.00 0.00 32.06 2.62
2495 2538 3.758023 TCACTTGGATCGTTGCATCAAAT 59.242 39.130 0.00 0.00 0.00 2.32
2496 2539 3.058293 GTCACTTGGATCGTTGCATCAAA 60.058 43.478 0.00 0.00 0.00 2.69
2497 2540 2.483877 GTCACTTGGATCGTTGCATCAA 59.516 45.455 0.00 0.00 0.00 2.57
2498 2541 2.076100 GTCACTTGGATCGTTGCATCA 58.924 47.619 0.00 0.00 0.00 3.07
2499 2542 1.398390 GGTCACTTGGATCGTTGCATC 59.602 52.381 0.00 0.00 0.00 3.91
2500 2543 1.453155 GGTCACTTGGATCGTTGCAT 58.547 50.000 0.00 0.00 0.00 3.96
2501 2544 0.605319 GGGTCACTTGGATCGTTGCA 60.605 55.000 0.00 0.00 0.00 4.08
2502 2545 1.635663 CGGGTCACTTGGATCGTTGC 61.636 60.000 0.00 0.00 0.00 4.17
2503 2546 0.320421 ACGGGTCACTTGGATCGTTG 60.320 55.000 0.00 0.00 35.68 4.10
2504 2547 0.320421 CACGGGTCACTTGGATCGTT 60.320 55.000 0.00 0.00 36.56 3.85
2505 2548 1.292223 CACGGGTCACTTGGATCGT 59.708 57.895 0.00 0.00 38.27 3.73
2506 2549 0.320421 AACACGGGTCACTTGGATCG 60.320 55.000 0.00 0.00 0.00 3.69
2507 2550 1.156736 CAACACGGGTCACTTGGATC 58.843 55.000 0.00 0.00 0.00 3.36
2508 2551 0.889186 GCAACACGGGTCACTTGGAT 60.889 55.000 0.00 0.00 0.00 3.41
2509 2552 1.525077 GCAACACGGGTCACTTGGA 60.525 57.895 0.00 0.00 0.00 3.53
2510 2553 0.250124 TAGCAACACGGGTCACTTGG 60.250 55.000 0.00 0.00 0.00 3.61
2511 2554 1.588674 TTAGCAACACGGGTCACTTG 58.411 50.000 0.00 0.00 0.00 3.16
2512 2555 2.335316 TTTAGCAACACGGGTCACTT 57.665 45.000 0.00 0.00 0.00 3.16
2513 2556 2.423577 GATTTAGCAACACGGGTCACT 58.576 47.619 0.00 0.00 0.00 3.41
2514 2557 1.127951 CGATTTAGCAACACGGGTCAC 59.872 52.381 0.00 0.00 0.00 3.67
2515 2558 1.001068 TCGATTTAGCAACACGGGTCA 59.999 47.619 0.00 0.00 0.00 4.02
2516 2559 1.659098 CTCGATTTAGCAACACGGGTC 59.341 52.381 0.00 0.00 0.00 4.46
2517 2560 1.722011 CTCGATTTAGCAACACGGGT 58.278 50.000 0.00 0.00 0.00 5.28
2518 2561 0.373716 GCTCGATTTAGCAACACGGG 59.626 55.000 0.00 0.00 42.30 5.28
2519 2562 1.359848 AGCTCGATTTAGCAACACGG 58.640 50.000 0.00 0.00 45.30 4.94
2520 2563 3.155998 CAAAGCTCGATTTAGCAACACG 58.844 45.455 0.00 0.00 45.30 4.49
2521 2564 2.911102 GCAAAGCTCGATTTAGCAACAC 59.089 45.455 0.00 0.00 45.30 3.32
2522 2565 2.412716 CGCAAAGCTCGATTTAGCAACA 60.413 45.455 0.00 0.00 45.30 3.33
2523 2566 2.169179 CGCAAAGCTCGATTTAGCAAC 58.831 47.619 0.00 0.00 45.30 4.17
2524 2567 1.804151 ACGCAAAGCTCGATTTAGCAA 59.196 42.857 0.00 0.00 45.30 3.91
2525 2568 1.438651 ACGCAAAGCTCGATTTAGCA 58.561 45.000 0.00 0.00 45.30 3.49
2526 2569 2.527442 AACGCAAAGCTCGATTTAGC 57.473 45.000 0.00 0.00 43.11 3.09
2527 2570 3.163594 CCAAACGCAAAGCTCGATTTAG 58.836 45.455 0.00 0.00 0.00 1.85
2528 2571 2.550606 ACCAAACGCAAAGCTCGATTTA 59.449 40.909 0.00 0.00 0.00 1.40
2529 2572 1.336755 ACCAAACGCAAAGCTCGATTT 59.663 42.857 0.00 0.00 0.00 2.17
2530 2573 0.951558 ACCAAACGCAAAGCTCGATT 59.048 45.000 0.00 0.00 0.00 3.34
2531 2574 0.517316 GACCAAACGCAAAGCTCGAT 59.483 50.000 0.00 0.00 0.00 3.59
2532 2575 0.531974 AGACCAAACGCAAAGCTCGA 60.532 50.000 0.00 0.00 0.00 4.04
2533 2576 0.307760 AAGACCAAACGCAAAGCTCG 59.692 50.000 0.00 0.00 0.00 5.03
2534 2577 2.350484 GGTAAGACCAAACGCAAAGCTC 60.350 50.000 0.00 0.00 38.42 4.09
2535 2578 1.607148 GGTAAGACCAAACGCAAAGCT 59.393 47.619 0.00 0.00 38.42 3.74
2536 2579 2.046283 GGTAAGACCAAACGCAAAGC 57.954 50.000 0.00 0.00 38.42 3.51
2554 2597 3.368323 GGTGAAGCAACCAACCAATATGG 60.368 47.826 0.00 0.00 40.93 2.74
2555 2598 3.848726 GGTGAAGCAACCAACCAATATG 58.151 45.455 0.00 0.00 40.22 1.78
2565 2608 1.401539 GCGAAAGATGGTGAAGCAACC 60.402 52.381 0.00 0.00 40.94 3.77
2566 2609 1.401539 GGCGAAAGATGGTGAAGCAAC 60.402 52.381 0.00 0.00 0.00 4.17
2567 2610 0.881118 GGCGAAAGATGGTGAAGCAA 59.119 50.000 0.00 0.00 0.00 3.91
2568 2611 0.036732 AGGCGAAAGATGGTGAAGCA 59.963 50.000 0.00 0.00 0.00 3.91
2569 2612 0.729690 GAGGCGAAAGATGGTGAAGC 59.270 55.000 0.00 0.00 0.00 3.86
2570 2613 1.002366 CGAGGCGAAAGATGGTGAAG 58.998 55.000 0.00 0.00 0.00 3.02
2571 2614 0.320374 ACGAGGCGAAAGATGGTGAA 59.680 50.000 0.00 0.00 0.00 3.18
2572 2615 0.108804 GACGAGGCGAAAGATGGTGA 60.109 55.000 0.00 0.00 0.00 4.02
2573 2616 0.389817 TGACGAGGCGAAAGATGGTG 60.390 55.000 0.00 0.00 0.00 4.17
2574 2617 0.537188 ATGACGAGGCGAAAGATGGT 59.463 50.000 0.00 0.00 0.00 3.55
2575 2618 2.509052 TATGACGAGGCGAAAGATGG 57.491 50.000 0.00 0.00 0.00 3.51
2576 2619 3.906998 AGATATGACGAGGCGAAAGATG 58.093 45.455 0.00 0.00 0.00 2.90
2577 2620 3.057174 GGAGATATGACGAGGCGAAAGAT 60.057 47.826 0.00 0.00 0.00 2.40
2578 2621 2.293677 GGAGATATGACGAGGCGAAAGA 59.706 50.000 0.00 0.00 0.00 2.52
2579 2622 2.294791 AGGAGATATGACGAGGCGAAAG 59.705 50.000 0.00 0.00 0.00 2.62
2580 2623 2.034685 CAGGAGATATGACGAGGCGAAA 59.965 50.000 0.00 0.00 0.00 3.46
2581 2624 1.609072 CAGGAGATATGACGAGGCGAA 59.391 52.381 0.00 0.00 0.00 4.70
2582 2625 1.239347 CAGGAGATATGACGAGGCGA 58.761 55.000 0.00 0.00 0.00 5.54
2583 2626 0.955178 ACAGGAGATATGACGAGGCG 59.045 55.000 0.00 0.00 0.00 5.52
2584 2627 5.899120 TTATACAGGAGATATGACGAGGC 57.101 43.478 0.00 0.00 0.00 4.70
2585 2628 7.976734 GGAAATTATACAGGAGATATGACGAGG 59.023 40.741 0.00 0.00 0.00 4.63
2586 2629 8.744652 AGGAAATTATACAGGAGATATGACGAG 58.255 37.037 0.00 0.00 0.00 4.18
2587 2630 8.523658 CAGGAAATTATACAGGAGATATGACGA 58.476 37.037 0.00 0.00 0.00 4.20
2588 2631 8.523658 TCAGGAAATTATACAGGAGATATGACG 58.476 37.037 0.00 0.00 0.00 4.35
2594 2637 7.446625 GCACAATCAGGAAATTATACAGGAGAT 59.553 37.037 0.00 0.00 0.00 2.75
2595 2638 6.767902 GCACAATCAGGAAATTATACAGGAGA 59.232 38.462 0.00 0.00 0.00 3.71
2596 2639 6.769822 AGCACAATCAGGAAATTATACAGGAG 59.230 38.462 0.00 0.00 0.00 3.69
2597 2640 6.662755 AGCACAATCAGGAAATTATACAGGA 58.337 36.000 0.00 0.00 0.00 3.86
2598 2641 6.949352 AGCACAATCAGGAAATTATACAGG 57.051 37.500 0.00 0.00 0.00 4.00
2599 2642 7.765307 ACAAGCACAATCAGGAAATTATACAG 58.235 34.615 0.00 0.00 0.00 2.74
2600 2643 7.701539 ACAAGCACAATCAGGAAATTATACA 57.298 32.000 0.00 0.00 0.00 2.29
2601 2644 8.028938 ACAACAAGCACAATCAGGAAATTATAC 58.971 33.333 0.00 0.00 0.00 1.47
2602 2645 8.028354 CACAACAAGCACAATCAGGAAATTATA 58.972 33.333 0.00 0.00 0.00 0.98
2603 2646 6.869913 CACAACAAGCACAATCAGGAAATTAT 59.130 34.615 0.00 0.00 0.00 1.28
2604 2647 6.183360 ACACAACAAGCACAATCAGGAAATTA 60.183 34.615 0.00 0.00 0.00 1.40
2605 2648 5.051816 CACAACAAGCACAATCAGGAAATT 58.948 37.500 0.00 0.00 0.00 1.82
2606 2649 4.099881 ACACAACAAGCACAATCAGGAAAT 59.900 37.500 0.00 0.00 0.00 2.17
2607 2650 3.446873 ACACAACAAGCACAATCAGGAAA 59.553 39.130 0.00 0.00 0.00 3.13
2608 2651 3.023119 ACACAACAAGCACAATCAGGAA 58.977 40.909 0.00 0.00 0.00 3.36
2609 2652 2.358582 CACACAACAAGCACAATCAGGA 59.641 45.455 0.00 0.00 0.00 3.86
2610 2653 2.099592 ACACACAACAAGCACAATCAGG 59.900 45.455 0.00 0.00 0.00 3.86
2611 2654 3.425577 ACACACAACAAGCACAATCAG 57.574 42.857 0.00 0.00 0.00 2.90
2612 2655 3.865011 AACACACAACAAGCACAATCA 57.135 38.095 0.00 0.00 0.00 2.57
2613 2656 3.925913 ACAAACACACAACAAGCACAATC 59.074 39.130 0.00 0.00 0.00 2.67
2614 2657 3.679025 CACAAACACACAACAAGCACAAT 59.321 39.130 0.00 0.00 0.00 2.71
2615 2658 3.055591 CACAAACACACAACAAGCACAA 58.944 40.909 0.00 0.00 0.00 3.33
2616 2659 2.608998 CCACAAACACACAACAAGCACA 60.609 45.455 0.00 0.00 0.00 4.57
2617 2660 1.991965 CCACAAACACACAACAAGCAC 59.008 47.619 0.00 0.00 0.00 4.40
2618 2661 1.615883 ACCACAAACACACAACAAGCA 59.384 42.857 0.00 0.00 0.00 3.91
2619 2662 2.094752 AGACCACAAACACACAACAAGC 60.095 45.455 0.00 0.00 0.00 4.01
2620 2663 3.848272 AGACCACAAACACACAACAAG 57.152 42.857 0.00 0.00 0.00 3.16
2621 2664 4.302455 CAAAGACCACAAACACACAACAA 58.698 39.130 0.00 0.00 0.00 2.83
2622 2665 3.858877 GCAAAGACCACAAACACACAACA 60.859 43.478 0.00 0.00 0.00 3.33
2623 2666 2.666022 GCAAAGACCACAAACACACAAC 59.334 45.455 0.00 0.00 0.00 3.32
2624 2667 2.560542 AGCAAAGACCACAAACACACAA 59.439 40.909 0.00 0.00 0.00 3.33
2639 2682 1.536766 TCATCGTCCAAAGCAGCAAAG 59.463 47.619 0.00 0.00 0.00 2.77
2640 2683 1.536766 CTCATCGTCCAAAGCAGCAAA 59.463 47.619 0.00 0.00 0.00 3.68
2641 2684 1.159285 CTCATCGTCCAAAGCAGCAA 58.841 50.000 0.00 0.00 0.00 3.91
2653 2696 1.244697 ACGGCACTCTGTCTCATCGT 61.245 55.000 0.00 0.00 0.00 3.73
2713 2790 8.599624 AAATTCCAATCATCAACCTGATAGTT 57.400 30.769 0.00 0.00 34.28 2.24
2715 2792 9.956720 GTAAAATTCCAATCATCAACCTGATAG 57.043 33.333 0.00 0.00 34.28 2.08
2716 2793 9.473007 TGTAAAATTCCAATCATCAACCTGATA 57.527 29.630 0.00 0.00 34.28 2.15
2719 2796 6.527722 CGTGTAAAATTCCAATCATCAACCTG 59.472 38.462 0.00 0.00 0.00 4.00
2723 2800 6.207614 TGGACGTGTAAAATTCCAATCATCAA 59.792 34.615 0.00 0.00 35.13 2.57
2725 2802 6.189677 TGGACGTGTAAAATTCCAATCATC 57.810 37.500 0.00 0.00 35.13 2.92
2727 2804 6.392625 TTTGGACGTGTAAAATTCCAATCA 57.607 33.333 0.00 0.00 45.40 2.57
2728 2805 8.973835 TTATTTGGACGTGTAAAATTCCAATC 57.026 30.769 0.00 0.00 45.40 2.67
2729 2806 9.765795 TTTTATTTGGACGTGTAAAATTCCAAT 57.234 25.926 0.00 0.00 45.40 3.16
2730 2807 9.032420 GTTTTATTTGGACGTGTAAAATTCCAA 57.968 29.630 0.00 0.00 44.62 3.53
2775 2879 1.005037 TAGGTCCAGCACGCTTGTG 60.005 57.895 0.00 0.00 46.67 3.33
2777 2881 2.103042 GCTAGGTCCAGCACGCTTG 61.103 63.158 8.05 0.00 41.40 4.01
2778 2882 2.266055 GCTAGGTCCAGCACGCTT 59.734 61.111 8.05 0.00 41.40 4.68
2779 2883 2.681778 AGCTAGGTCCAGCACGCT 60.682 61.111 13.61 0.00 44.35 5.07
2780 2884 1.945354 TACAGCTAGGTCCAGCACGC 61.945 60.000 13.61 0.00 44.35 5.34
2826 2937 2.044555 TCGTCCTCCGCGTTGAGAT 61.045 57.895 13.15 0.00 34.11 2.75
2827 2938 2.670592 TCGTCCTCCGCGTTGAGA 60.671 61.111 13.15 0.00 34.11 3.27


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

AutoCloner maintained by Alex Coulton.