Multiple sequence alignment - TraesCS3A01G186000

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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 TraesCS3A01G186000 chr3A 100.000 3245 0 0 1 3245 219725444 219728688 0.000000e+00 5993.0
1 TraesCS3A01G186000 chr3D 96.355 2414 59 9 107 2508 178405402 178407798 0.000000e+00 3943.0
2 TraesCS3A01G186000 chr3D 97.802 91 2 0 1 91 178405329 178405419 1.210000e-34 158.0
3 TraesCS3A01G186000 chr3B 96.030 2418 79 7 107 2508 256728241 256730657 0.000000e+00 3917.0
4 TraesCS3A01G186000 chr3B 94.643 56 3 0 1549 1604 5598659 5598714 1.600000e-13 87.9
5 TraesCS3A01G186000 chr3B 93.103 58 2 2 39 96 256728207 256728262 2.070000e-12 84.2
6 TraesCS3A01G186000 chr4D 87.242 533 64 4 2712 3243 42101917 42101388 3.580000e-169 604.0
7 TraesCS3A01G186000 chr2B 93.575 358 20 1 1461 1818 33755746 33755392 6.160000e-147 531.0
8 TraesCS3A01G186000 chr6A 90.659 364 31 1 1461 1824 508057618 508057978 6.300000e-132 481.0
9 TraesCS3A01G186000 chr6A 88.312 385 37 5 1444 1824 508131000 508131380 3.820000e-124 455.0
10 TraesCS3A01G186000 chr5D 96.032 126 5 0 1740 1865 42975332 42975457 4.240000e-49 206.0
11 TraesCS3A01G186000 chr5D 94.118 119 6 1 1968 2086 42975452 42975569 2.570000e-41 180.0
12 TraesCS3A01G186000 chr1D 94.783 115 6 0 1823 1937 451260655 451260769 2.570000e-41 180.0
13 TraesCS3A01G186000 chr4B 93.056 72 5 0 1740 1811 385938707 385938778 4.430000e-19 106.0
14 TraesCS3A01G186000 chr7A 93.548 62 4 0 1549 1610 623459907 623459968 3.450000e-15 93.5
15 TraesCS3A01G186000 chrUn 94.643 56 3 0 1549 1604 464945795 464945740 1.600000e-13 87.9
16 TraesCS3A01G186000 chr7B 93.878 49 2 1 1444 1492 570266847 570266894 4.490000e-09 73.1
17 TraesCS3A01G186000 chr7B 91.837 49 3 1 1444 1492 605428519 605428472 2.090000e-07 67.6
18 TraesCS3A01G186000 chr1B 97.619 42 1 0 1451 1492 583126963 583127004 4.490000e-09 73.1
19 TraesCS3A01G186000 chr1B 93.878 49 2 1 1444 1492 649692735 649692782 4.490000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G186000 chr3A 219725444 219728688 3244 False 5993.0 5993 100.0000 1 3245 1 chr3A.!!$F1 3244
1 TraesCS3A01G186000 chr3D 178405329 178407798 2469 False 2050.5 3943 97.0785 1 2508 2 chr3D.!!$F1 2507
2 TraesCS3A01G186000 chr3B 256728207 256730657 2450 False 2000.6 3917 94.5665 39 2508 2 chr3B.!!$F2 2469
3 TraesCS3A01G186000 chr4D 42101388 42101917 529 True 604.0 604 87.2420 2712 3243 1 chr4D.!!$R1 531

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
910 922 0.110295 TACAGTGCACATGCCACCTT 59.89 50.0 21.04 0.52 41.18 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2573 2589 0.107557 AACCGAGACGTTGGGTTTGT 60.108 50.0 11.62 0.0 44.52 2.83 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
52 53 4.750598 GCCCGACTATTAGAATCAACCTTC 59.249 45.833 0.00 0.00 0.00 3.46
92 93 6.360370 TGGTAACAGAAGAAGATTAGTGCT 57.640 37.500 0.00 0.00 46.17 4.40
93 94 7.476540 TGGTAACAGAAGAAGATTAGTGCTA 57.523 36.000 0.00 0.00 46.17 3.49
94 95 7.548097 TGGTAACAGAAGAAGATTAGTGCTAG 58.452 38.462 0.00 0.00 46.17 3.42
95 96 7.178628 TGGTAACAGAAGAAGATTAGTGCTAGT 59.821 37.037 0.00 0.00 46.17 2.57
96 97 7.703197 GGTAACAGAAGAAGATTAGTGCTAGTC 59.297 40.741 0.00 0.00 0.00 2.59
97 98 6.842437 ACAGAAGAAGATTAGTGCTAGTCA 57.158 37.500 4.88 0.00 0.00 3.41
98 99 7.233389 ACAGAAGAAGATTAGTGCTAGTCAA 57.767 36.000 4.88 0.00 0.00 3.18
99 100 7.671302 ACAGAAGAAGATTAGTGCTAGTCAAA 58.329 34.615 4.88 0.00 0.00 2.69
100 101 8.150945 ACAGAAGAAGATTAGTGCTAGTCAAAA 58.849 33.333 4.88 0.00 0.00 2.44
101 102 8.993121 CAGAAGAAGATTAGTGCTAGTCAAAAA 58.007 33.333 4.88 0.00 0.00 1.94
232 233 0.187606 ACCTTCCAAGTTCCAACCCC 59.812 55.000 0.00 0.00 0.00 4.95
273 274 2.939261 CGTCCGTGGCTTGGGTAGT 61.939 63.158 0.00 0.00 0.00 2.73
275 276 0.250597 GTCCGTGGCTTGGGTAGTTT 60.251 55.000 0.00 0.00 0.00 2.66
543 544 1.993391 AAAGATCGGGCCGGGAGAA 60.993 57.895 27.98 6.37 0.00 2.87
677 678 2.241430 TCTTCTACCCTGATCGTGGAGA 59.759 50.000 7.29 0.00 0.00 3.71
718 719 2.629656 GCACTGCCAATGCCTTCGT 61.630 57.895 0.00 0.00 37.08 3.85
723 724 2.334946 GCCAATGCCTTCGTCTGCA 61.335 57.895 0.00 0.00 42.52 4.41
853 854 4.461081 TGTAACAAGCCAGAAACACAAACT 59.539 37.500 0.00 0.00 0.00 2.66
905 917 6.098679 TGATTTAATTTACAGTGCACATGCC 58.901 36.000 21.04 0.00 41.18 4.40
906 918 5.459536 TTTAATTTACAGTGCACATGCCA 57.540 34.783 21.04 0.00 41.18 4.92
908 920 0.958091 TTTACAGTGCACATGCCACC 59.042 50.000 21.04 0.00 41.18 4.61
910 922 0.110295 TACAGTGCACATGCCACCTT 59.890 50.000 21.04 0.52 41.18 3.50
911 923 0.110295 ACAGTGCACATGCCACCTTA 59.890 50.000 21.04 0.00 41.18 2.69
912 924 1.272092 ACAGTGCACATGCCACCTTAT 60.272 47.619 21.04 0.00 41.18 1.73
913 925 1.133598 CAGTGCACATGCCACCTTATG 59.866 52.381 21.04 0.00 41.18 1.90
1092 1106 4.436998 GTCACCCAGCTCGACCGG 62.437 72.222 0.00 0.00 0.00 5.28
1128 1142 2.083774 GACAATCAGGAACGGAATGCA 58.916 47.619 0.00 0.00 36.94 3.96
1203 1217 4.803426 GCCTCTGACGACGCCCAG 62.803 72.222 10.53 10.53 0.00 4.45
1427 1441 1.067776 GTCTTCTCCATCGACCAACGT 60.068 52.381 0.00 0.00 43.13 3.99
1599 1613 3.740397 CACCACTACGACGCCGGA 61.740 66.667 5.05 0.00 40.78 5.14
1653 1667 1.883084 GCACCGCGTAGGAATCCTG 60.883 63.158 12.96 0.00 45.00 3.86
1812 1826 3.878519 GAGGAGCTCGACGACCCG 61.879 72.222 7.83 0.00 0.00 5.28
1821 1835 1.059994 CGACGACCCGTACTTCGAG 59.940 63.158 13.38 5.35 41.37 4.04
1861 1875 4.812476 CGCGACCATTCTCCGGCA 62.812 66.667 0.00 0.00 0.00 5.69
1962 1976 2.029666 GCCATCCGGATCCTCACG 59.970 66.667 15.88 1.56 0.00 4.35
1963 1977 2.029666 CCATCCGGATCCTCACGC 59.970 66.667 15.88 0.00 0.00 5.34
2255 2269 0.643820 CTGAATTAACGCCGACGACC 59.356 55.000 0.00 0.00 43.93 4.79
2351 2367 1.344763 AGAGAAGCCTTGCGTGTTACT 59.655 47.619 0.00 0.00 0.00 2.24
2352 2368 1.727335 GAGAAGCCTTGCGTGTTACTC 59.273 52.381 0.00 0.00 0.00 2.59
2353 2369 0.796927 GAAGCCTTGCGTGTTACTCC 59.203 55.000 0.00 0.00 0.00 3.85
2377 2393 0.940833 TGTGTGTGTGCGTACATTGG 59.059 50.000 10.21 0.00 39.39 3.16
2411 2427 1.372499 TACGTGAGCTTGTGCCGTC 60.372 57.895 0.00 0.00 40.80 4.79
2474 2490 1.014352 GAGCTGACACCAAACGTTGT 58.986 50.000 0.00 0.00 0.00 3.32
2501 2517 1.700523 CCAACACAATGCATTGGACG 58.299 50.000 35.85 26.71 44.84 4.79
2504 2520 1.603456 ACACAATGCATTGGACGACA 58.397 45.000 35.85 0.00 41.96 4.35
2508 2524 1.978097 CAATGCATTGGACGACAAACG 59.022 47.619 28.34 1.25 43.46 3.60
2518 2534 2.823628 CGACAAACGTCCCCTTCTC 58.176 57.895 0.00 0.00 37.22 2.87
2519 2535 0.032952 CGACAAACGTCCCCTTCTCA 59.967 55.000 0.00 0.00 37.22 3.27
2520 2536 1.539496 CGACAAACGTCCCCTTCTCAA 60.539 52.381 0.00 0.00 37.22 3.02
2521 2537 2.143925 GACAAACGTCCCCTTCTCAAG 58.856 52.381 0.00 0.00 0.00 3.02
2522 2538 1.766496 ACAAACGTCCCCTTCTCAAGA 59.234 47.619 0.00 0.00 0.00 3.02
2523 2539 2.171870 ACAAACGTCCCCTTCTCAAGAA 59.828 45.455 0.00 0.00 0.00 2.52
2534 2550 4.458951 CTTCTCAAGAAGGTCAACGTTG 57.541 45.455 22.35 22.35 45.79 4.10
2535 2551 2.833794 TCTCAAGAAGGTCAACGTTGG 58.166 47.619 27.02 9.30 0.00 3.77
2536 2552 1.873591 CTCAAGAAGGTCAACGTTGGG 59.126 52.381 27.02 3.68 0.00 4.12
2537 2553 1.487142 TCAAGAAGGTCAACGTTGGGA 59.513 47.619 27.02 7.03 0.00 4.37
2538 2554 1.873591 CAAGAAGGTCAACGTTGGGAG 59.126 52.381 27.02 2.49 0.00 4.30
2539 2555 1.129058 AGAAGGTCAACGTTGGGAGT 58.871 50.000 27.02 11.30 0.00 3.85
2540 2556 1.202651 AGAAGGTCAACGTTGGGAGTG 60.203 52.381 27.02 2.01 0.00 3.51
2541 2557 0.834612 AAGGTCAACGTTGGGAGTGA 59.165 50.000 27.02 4.74 0.00 3.41
2542 2558 0.393077 AGGTCAACGTTGGGAGTGAG 59.607 55.000 27.02 0.00 0.00 3.51
2543 2559 1.228657 GGTCAACGTTGGGAGTGAGC 61.229 60.000 27.02 13.26 0.00 4.26
2544 2560 1.070786 TCAACGTTGGGAGTGAGCC 59.929 57.895 27.02 0.00 0.00 4.70
2545 2561 1.071471 CAACGTTGGGAGTGAGCCT 59.929 57.895 20.71 0.00 0.00 4.58
2546 2562 1.071471 AACGTTGGGAGTGAGCCTG 59.929 57.895 0.00 0.00 0.00 4.85
2547 2563 2.046892 CGTTGGGAGTGAGCCTGG 60.047 66.667 0.00 0.00 0.00 4.45
2548 2564 2.360475 GTTGGGAGTGAGCCTGGC 60.360 66.667 11.65 11.65 0.00 4.85
2549 2565 2.530151 TTGGGAGTGAGCCTGGCT 60.530 61.111 23.64 23.64 43.88 4.75
2559 2575 2.662309 AGCCTGGCTCAATTGGTTG 58.338 52.632 17.22 0.00 30.62 3.77
2560 2576 0.112995 AGCCTGGCTCAATTGGTTGA 59.887 50.000 17.22 0.00 41.89 3.18
2561 2577 0.968405 GCCTGGCTCAATTGGTTGAA 59.032 50.000 12.43 0.00 43.39 2.69
2562 2578 1.067354 GCCTGGCTCAATTGGTTGAAG 60.067 52.381 12.43 0.00 43.39 3.02
2563 2579 1.547372 CCTGGCTCAATTGGTTGAAGG 59.453 52.381 5.42 3.46 43.39 3.46
2564 2580 2.517959 CTGGCTCAATTGGTTGAAGGA 58.482 47.619 5.42 0.00 43.39 3.36
2565 2581 2.490903 CTGGCTCAATTGGTTGAAGGAG 59.509 50.000 5.42 0.00 43.39 3.69
2566 2582 2.158475 TGGCTCAATTGGTTGAAGGAGT 60.158 45.455 5.42 0.00 43.39 3.85
2567 2583 2.229784 GGCTCAATTGGTTGAAGGAGTG 59.770 50.000 5.42 0.00 43.39 3.51
2568 2584 2.229784 GCTCAATTGGTTGAAGGAGTGG 59.770 50.000 5.42 0.00 43.39 4.00
2569 2585 3.754965 CTCAATTGGTTGAAGGAGTGGA 58.245 45.455 5.42 0.00 43.39 4.02
2570 2586 4.338879 CTCAATTGGTTGAAGGAGTGGAT 58.661 43.478 5.42 0.00 43.39 3.41
2571 2587 4.081406 TCAATTGGTTGAAGGAGTGGATG 58.919 43.478 5.42 0.00 41.22 3.51
2572 2588 3.814504 ATTGGTTGAAGGAGTGGATGT 57.185 42.857 0.00 0.00 0.00 3.06
2573 2589 4.927267 ATTGGTTGAAGGAGTGGATGTA 57.073 40.909 0.00 0.00 0.00 2.29
2574 2590 3.695830 TGGTTGAAGGAGTGGATGTAC 57.304 47.619 0.00 0.00 0.00 2.90
2575 2591 2.976185 TGGTTGAAGGAGTGGATGTACA 59.024 45.455 0.00 0.00 0.00 2.90
2576 2592 3.392947 TGGTTGAAGGAGTGGATGTACAA 59.607 43.478 0.00 0.00 0.00 2.41
2577 2593 4.141367 TGGTTGAAGGAGTGGATGTACAAA 60.141 41.667 0.00 0.00 0.00 2.83
2578 2594 4.215613 GGTTGAAGGAGTGGATGTACAAAC 59.784 45.833 0.00 0.00 0.00 2.93
2579 2595 4.015872 TGAAGGAGTGGATGTACAAACC 57.984 45.455 13.39 13.39 0.00 3.27
2580 2596 3.244770 TGAAGGAGTGGATGTACAAACCC 60.245 47.826 16.34 11.22 0.00 4.11
2581 2597 2.344592 AGGAGTGGATGTACAAACCCA 58.655 47.619 16.34 13.27 0.00 4.51
2582 2598 2.714250 AGGAGTGGATGTACAAACCCAA 59.286 45.455 14.17 0.00 0.00 4.12
2583 2599 2.817844 GGAGTGGATGTACAAACCCAAC 59.182 50.000 14.17 9.51 0.00 3.77
2584 2600 2.482721 GAGTGGATGTACAAACCCAACG 59.517 50.000 14.17 0.00 0.00 4.10
2585 2601 2.158726 AGTGGATGTACAAACCCAACGT 60.159 45.455 14.17 0.00 0.00 3.99
2586 2602 2.224784 GTGGATGTACAAACCCAACGTC 59.775 50.000 14.17 0.00 0.00 4.34
2587 2603 2.105134 TGGATGTACAAACCCAACGTCT 59.895 45.455 16.34 0.00 31.29 4.18
2588 2604 2.740447 GGATGTACAAACCCAACGTCTC 59.260 50.000 0.00 0.00 31.29 3.36
2589 2605 1.855513 TGTACAAACCCAACGTCTCG 58.144 50.000 0.00 0.00 0.00 4.04
2590 2606 1.142474 GTACAAACCCAACGTCTCGG 58.858 55.000 0.00 0.00 0.00 4.63
2591 2607 0.752054 TACAAACCCAACGTCTCGGT 59.248 50.000 0.00 0.00 0.00 4.69
2592 2608 0.107557 ACAAACCCAACGTCTCGGTT 60.108 50.000 7.81 7.81 41.68 4.44
2593 2609 0.584876 CAAACCCAACGTCTCGGTTC 59.415 55.000 12.66 0.00 38.96 3.62
2594 2610 0.178533 AAACCCAACGTCTCGGTTCA 59.821 50.000 12.66 0.00 38.96 3.18
2595 2611 0.178533 AACCCAACGTCTCGGTTCAA 59.821 50.000 7.81 0.00 34.80 2.69
2596 2612 0.178533 ACCCAACGTCTCGGTTCAAA 59.821 50.000 0.00 0.00 0.00 2.69
2597 2613 1.202722 ACCCAACGTCTCGGTTCAAAT 60.203 47.619 0.00 0.00 0.00 2.32
2598 2614 1.463444 CCCAACGTCTCGGTTCAAATC 59.537 52.381 0.00 0.00 0.00 2.17
2599 2615 1.463444 CCAACGTCTCGGTTCAAATCC 59.537 52.381 0.00 0.00 0.00 3.01
2600 2616 2.413837 CAACGTCTCGGTTCAAATCCT 58.586 47.619 0.00 0.00 0.00 3.24
2601 2617 2.365408 ACGTCTCGGTTCAAATCCTC 57.635 50.000 0.00 0.00 0.00 3.71
2602 2618 1.616865 ACGTCTCGGTTCAAATCCTCA 59.383 47.619 0.00 0.00 0.00 3.86
2603 2619 1.993370 CGTCTCGGTTCAAATCCTCAC 59.007 52.381 0.00 0.00 0.00 3.51
2604 2620 1.993370 GTCTCGGTTCAAATCCTCACG 59.007 52.381 0.00 0.00 0.00 4.35
2605 2621 1.067142 TCTCGGTTCAAATCCTCACGG 60.067 52.381 0.00 0.00 0.00 4.94
2606 2622 0.970640 TCGGTTCAAATCCTCACGGA 59.029 50.000 0.00 0.00 45.16 4.69
2607 2623 1.067142 TCGGTTCAAATCCTCACGGAG 60.067 52.381 0.00 0.00 44.06 4.63
2615 2631 2.584608 CCTCACGGAGGCGGATTT 59.415 61.111 6.97 0.00 43.29 2.17
2616 2632 1.820581 CCTCACGGAGGCGGATTTA 59.179 57.895 6.97 0.00 43.29 1.40
2617 2633 0.249489 CCTCACGGAGGCGGATTTAG 60.249 60.000 6.97 0.00 43.29 1.85
2618 2634 0.249489 CTCACGGAGGCGGATTTAGG 60.249 60.000 0.00 0.00 0.00 2.69
2619 2635 0.974010 TCACGGAGGCGGATTTAGGT 60.974 55.000 0.00 0.00 0.00 3.08
2620 2636 0.107848 CACGGAGGCGGATTTAGGTT 60.108 55.000 0.00 0.00 0.00 3.50
2621 2637 0.616891 ACGGAGGCGGATTTAGGTTT 59.383 50.000 0.00 0.00 0.00 3.27
2622 2638 1.296727 CGGAGGCGGATTTAGGTTTC 58.703 55.000 0.00 0.00 0.00 2.78
2623 2639 1.134491 CGGAGGCGGATTTAGGTTTCT 60.134 52.381 0.00 0.00 0.00 2.52
2624 2640 2.101917 CGGAGGCGGATTTAGGTTTCTA 59.898 50.000 0.00 0.00 0.00 2.10
2625 2641 3.244112 CGGAGGCGGATTTAGGTTTCTAT 60.244 47.826 0.00 0.00 0.00 1.98
2626 2642 4.065789 GGAGGCGGATTTAGGTTTCTATG 58.934 47.826 0.00 0.00 0.00 2.23
2627 2643 4.444449 GGAGGCGGATTTAGGTTTCTATGT 60.444 45.833 0.00 0.00 0.00 2.29
2628 2644 5.112129 AGGCGGATTTAGGTTTCTATGTT 57.888 39.130 0.00 0.00 0.00 2.71
2629 2645 4.881850 AGGCGGATTTAGGTTTCTATGTTG 59.118 41.667 0.00 0.00 0.00 3.33
2630 2646 4.036380 GGCGGATTTAGGTTTCTATGTTGG 59.964 45.833 0.00 0.00 0.00 3.77
2631 2647 4.638865 GCGGATTTAGGTTTCTATGTTGGT 59.361 41.667 0.00 0.00 0.00 3.67
2632 2648 5.448632 GCGGATTTAGGTTTCTATGTTGGTG 60.449 44.000 0.00 0.00 0.00 4.17
2633 2649 5.448632 CGGATTTAGGTTTCTATGTTGGTGC 60.449 44.000 0.00 0.00 0.00 5.01
2634 2650 5.417580 GGATTTAGGTTTCTATGTTGGTGCA 59.582 40.000 0.00 0.00 0.00 4.57
2635 2651 5.957842 TTTAGGTTTCTATGTTGGTGCAG 57.042 39.130 0.00 0.00 0.00 4.41
2636 2652 3.788227 AGGTTTCTATGTTGGTGCAGA 57.212 42.857 0.00 0.00 0.00 4.26
2637 2653 3.679389 AGGTTTCTATGTTGGTGCAGAG 58.321 45.455 0.00 0.00 0.00 3.35
2638 2654 2.749621 GGTTTCTATGTTGGTGCAGAGG 59.250 50.000 0.00 0.00 0.00 3.69
2639 2655 2.113860 TTCTATGTTGGTGCAGAGGC 57.886 50.000 0.00 0.00 41.68 4.70
2640 2656 1.279496 TCTATGTTGGTGCAGAGGCT 58.721 50.000 0.00 0.00 41.91 4.58
2641 2657 1.065926 TCTATGTTGGTGCAGAGGCTG 60.066 52.381 0.00 0.00 41.91 4.85
2642 2658 0.983467 TATGTTGGTGCAGAGGCTGA 59.017 50.000 0.00 0.00 41.91 4.26
2643 2659 0.322277 ATGTTGGTGCAGAGGCTGAG 60.322 55.000 0.00 0.00 41.91 3.35
2644 2660 1.372683 GTTGGTGCAGAGGCTGAGA 59.627 57.895 0.00 0.00 41.91 3.27
2645 2661 0.673022 GTTGGTGCAGAGGCTGAGAG 60.673 60.000 0.00 0.00 41.91 3.20
2646 2662 0.833409 TTGGTGCAGAGGCTGAGAGA 60.833 55.000 0.00 0.00 41.91 3.10
2647 2663 1.256361 TGGTGCAGAGGCTGAGAGAG 61.256 60.000 0.00 0.00 41.91 3.20
2672 2688 2.885113 GCGGATTTTGCCCCTCAC 59.115 61.111 0.00 0.00 0.00 3.51
2673 2689 1.976474 GCGGATTTTGCCCCTCACA 60.976 57.895 0.00 0.00 0.00 3.58
2674 2690 1.883021 CGGATTTTGCCCCTCACAC 59.117 57.895 0.00 0.00 0.00 3.82
2675 2691 0.609131 CGGATTTTGCCCCTCACACT 60.609 55.000 0.00 0.00 0.00 3.55
2676 2692 0.890683 GGATTTTGCCCCTCACACTG 59.109 55.000 0.00 0.00 0.00 3.66
2677 2693 1.620822 GATTTTGCCCCTCACACTGT 58.379 50.000 0.00 0.00 0.00 3.55
2678 2694 1.963515 GATTTTGCCCCTCACACTGTT 59.036 47.619 0.00 0.00 0.00 3.16
2679 2695 2.738587 TTTTGCCCCTCACACTGTTA 57.261 45.000 0.00 0.00 0.00 2.41
2680 2696 2.969821 TTTGCCCCTCACACTGTTAT 57.030 45.000 0.00 0.00 0.00 1.89
2681 2697 4.374689 TTTTGCCCCTCACACTGTTATA 57.625 40.909 0.00 0.00 0.00 0.98
2682 2698 3.343941 TTGCCCCTCACACTGTTATAC 57.656 47.619 0.00 0.00 0.00 1.47
2683 2699 1.557832 TGCCCCTCACACTGTTATACC 59.442 52.381 0.00 0.00 0.00 2.73
2684 2700 1.838077 GCCCCTCACACTGTTATACCT 59.162 52.381 0.00 0.00 0.00 3.08
2685 2701 2.238898 GCCCCTCACACTGTTATACCTT 59.761 50.000 0.00 0.00 0.00 3.50
2686 2702 3.681874 GCCCCTCACACTGTTATACCTTC 60.682 52.174 0.00 0.00 0.00 3.46
2687 2703 3.430374 CCCCTCACACTGTTATACCTTCG 60.430 52.174 0.00 0.00 0.00 3.79
2688 2704 3.194968 CCCTCACACTGTTATACCTTCGT 59.805 47.826 0.00 0.00 0.00 3.85
2689 2705 4.322499 CCCTCACACTGTTATACCTTCGTT 60.322 45.833 0.00 0.00 0.00 3.85
2690 2706 5.105635 CCCTCACACTGTTATACCTTCGTTA 60.106 44.000 0.00 0.00 0.00 3.18
2691 2707 5.803967 CCTCACACTGTTATACCTTCGTTAC 59.196 44.000 0.00 0.00 0.00 2.50
2692 2708 5.393124 TCACACTGTTATACCTTCGTTACG 58.607 41.667 0.00 0.00 0.00 3.18
2693 2709 5.181056 TCACACTGTTATACCTTCGTTACGA 59.819 40.000 2.33 2.33 0.00 3.43
2694 2710 5.284660 CACACTGTTATACCTTCGTTACGAC 59.715 44.000 7.06 0.00 34.89 4.34
2703 2719 4.125097 CGTTACGACGTTGGCGGC 62.125 66.667 5.50 0.00 44.08 6.53
2722 2738 1.709147 CGGCTCCTTGCTTTGATCCG 61.709 60.000 0.00 0.00 42.39 4.18
2728 2744 1.915614 CTTGCTTTGATCCGTGCGCT 61.916 55.000 9.73 0.00 0.00 5.92
2830 2846 4.415150 ATGCGGGCAGAGGTGGTG 62.415 66.667 0.00 0.00 0.00 4.17
2860 2876 1.883275 CTCGGCTATCGTCCAGATCTT 59.117 52.381 0.00 0.00 40.66 2.40
2863 2879 2.552743 CGGCTATCGTCCAGATCTTACA 59.447 50.000 0.00 0.00 40.66 2.41
2864 2880 3.004419 CGGCTATCGTCCAGATCTTACAA 59.996 47.826 0.00 0.00 40.66 2.41
2870 2886 2.098607 CGTCCAGATCTTACAACGGCTA 59.901 50.000 0.00 0.00 0.00 3.93
2994 3010 2.333926 CGCTGTCGTGAATAAAGGTGA 58.666 47.619 0.00 0.00 0.00 4.02
2995 3011 2.930040 CGCTGTCGTGAATAAAGGTGAT 59.070 45.455 0.00 0.00 0.00 3.06
2998 3014 3.006940 TGTCGTGAATAAAGGTGATGGC 58.993 45.455 0.00 0.00 0.00 4.40
3013 3029 3.435186 GGCCCTCGTGCTTTGCTC 61.435 66.667 0.00 0.00 0.00 4.26
3019 3035 1.357258 CTCGTGCTTTGCTCGCATCT 61.357 55.000 8.80 0.00 43.69 2.90
3022 3038 2.102438 TGCTTTGCTCGCATCTCGG 61.102 57.895 0.00 0.00 39.05 4.63
3040 3056 2.463620 GCAACGCTCGGCATGATCA 61.464 57.895 0.00 0.00 0.00 2.92
3041 3057 1.980951 GCAACGCTCGGCATGATCAA 61.981 55.000 0.00 0.00 0.00 2.57
3043 3059 0.673333 AACGCTCGGCATGATCAACA 60.673 50.000 0.00 0.00 0.00 3.33
3083 3099 0.951040 CGGGTTCTGGAACTGCTGAC 60.951 60.000 12.34 0.00 40.94 3.51
3085 3101 0.033504 GGTTCTGGAACTGCTGACGA 59.966 55.000 12.34 0.00 40.94 4.20
3093 3109 2.606725 GGAACTGCTGACGATGATCTTG 59.393 50.000 0.00 0.00 0.00 3.02
3096 3112 0.462581 TGCTGACGATGATCTTGCCC 60.463 55.000 0.00 0.00 0.00 5.36
3130 3146 1.663739 GATAGTATCCGGCCGTGCA 59.336 57.895 26.12 7.89 0.00 4.57
3148 3164 1.127951 GCACGTCCAAATCAACCTACG 59.872 52.381 0.00 0.00 36.48 3.51
3163 3179 2.615262 CTACGAGGTTCTGAGGGCGC 62.615 65.000 0.00 0.00 0.00 6.53
3217 3233 4.810191 GGACATATAGGCCTCTCGATTT 57.190 45.455 9.68 0.00 44.70 2.17
3218 3234 5.153950 GGACATATAGGCCTCTCGATTTT 57.846 43.478 9.68 0.00 44.70 1.82
3225 3241 2.158842 AGGCCTCTCGATTTTCATGGAG 60.159 50.000 0.00 0.00 36.75 3.86
3231 3247 5.163509 CCTCTCGATTTTCATGGAGTAGACA 60.164 44.000 0.00 0.00 36.77 3.41
3232 3248 6.462207 CCTCTCGATTTTCATGGAGTAGACAT 60.462 42.308 0.00 0.00 36.77 3.06
3238 3254 5.852282 TTTCATGGAGTAGACATCGATGA 57.148 39.130 31.33 6.81 39.29 2.92
3243 3259 5.506686 TGGAGTAGACATCGATGAAGAAG 57.493 43.478 31.33 4.40 0.00 2.85
3244 3260 4.339530 TGGAGTAGACATCGATGAAGAAGG 59.660 45.833 31.33 3.61 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.674796 AGTCGGGCATGTCTAACTTC 57.325 50.000 0.00 0.00 0.00 3.01
52 53 5.064962 TGTTACCATTTTAACCGGCTAATCG 59.935 40.000 0.00 0.00 31.87 3.34
106 107 9.482175 AGTATACTCCACTAATCTTCTTCTGTT 57.518 33.333 0.00 0.00 0.00 3.16
107 108 9.482175 AAGTATACTCCACTAATCTTCTTCTGT 57.518 33.333 5.70 0.00 0.00 3.41
108 109 9.959749 GAAGTATACTCCACTAATCTTCTTCTG 57.040 37.037 5.70 0.00 0.00 3.02
109 110 9.702253 TGAAGTATACTCCACTAATCTTCTTCT 57.298 33.333 5.70 0.00 33.57 2.85
110 111 9.959749 CTGAAGTATACTCCACTAATCTTCTTC 57.040 37.037 5.70 0.00 33.57 2.87
111 112 9.702253 TCTGAAGTATACTCCACTAATCTTCTT 57.298 33.333 5.70 0.00 33.57 2.52
273 274 2.033448 CTGCCTGGCCCGTACAAA 59.967 61.111 17.53 0.00 0.00 2.83
293 294 1.632422 CTAAATTTGGCGCTGGCTTG 58.368 50.000 7.64 0.00 39.81 4.01
296 297 1.519234 GGCTAAATTTGGCGCTGGC 60.519 57.895 18.80 0.00 35.26 4.85
301 302 2.976271 GCCATGGCTAAATTTGGCG 58.024 52.632 29.98 7.48 44.58 5.69
442 443 4.722279 TCCTTCCCCTTCCTTTCTAATCTC 59.278 45.833 0.00 0.00 0.00 2.75
677 678 7.542130 GTGCGGAATTGATTTGATACTCTTTTT 59.458 33.333 0.00 0.00 0.00 1.94
769 770 4.476410 TCAGTAGCAGCCGTCGCG 62.476 66.667 0.00 0.00 41.18 5.87
853 854 1.293963 CGGAGACACGACGTACCTCA 61.294 60.000 22.18 0.00 35.47 3.86
906 918 5.338708 CCAACTTCCTCAGATCACATAAGGT 60.339 44.000 0.00 0.00 0.00 3.50
908 920 5.738909 ACCAACTTCCTCAGATCACATAAG 58.261 41.667 0.00 0.00 0.00 1.73
910 922 5.762179 AACCAACTTCCTCAGATCACATA 57.238 39.130 0.00 0.00 0.00 2.29
911 923 4.647564 AACCAACTTCCTCAGATCACAT 57.352 40.909 0.00 0.00 0.00 3.21
912 924 4.141505 TGAAACCAACTTCCTCAGATCACA 60.142 41.667 0.00 0.00 0.00 3.58
913 925 4.389374 TGAAACCAACTTCCTCAGATCAC 58.611 43.478 0.00 0.00 0.00 3.06
1143 1157 2.359404 GGGGAGGAGAGACACCGA 59.641 66.667 0.00 0.00 0.00 4.69
1203 1217 0.744771 GGGGCATCTTCTTGTCGTCC 60.745 60.000 0.00 0.00 0.00 4.79
1427 1441 4.478371 TCTCGTAGCCGCCTCCGA 62.478 66.667 0.00 0.00 36.29 4.55
1512 1526 1.989165 GATATCTTGATCAGCGCCGTC 59.011 52.381 2.29 0.00 0.00 4.79
1515 1529 1.731720 GGGATATCTTGATCAGCGCC 58.268 55.000 2.29 0.00 0.00 6.53
1599 1613 2.517402 CTAGACGGGCCGAGCTCT 60.517 66.667 35.78 26.40 0.00 4.09
1611 1625 1.744522 GAGGTCACGGAGAACCTAGAC 59.255 57.143 0.00 0.00 44.45 2.59
1644 1658 2.579201 CGCACGTCCAGGATTCCT 59.421 61.111 0.00 0.00 0.00 3.36
1794 1808 2.750637 GGGTCGTCGAGCTCCTCA 60.751 66.667 22.48 0.00 0.00 3.86
1798 1812 1.642952 AAGTACGGGTCGTCGAGCTC 61.643 60.000 22.48 2.73 41.54 4.09
1812 1826 2.446341 GTGCAGCCACTCGAAGTAC 58.554 57.895 0.00 0.00 38.93 2.73
1962 1976 2.029844 GAGGAAGACGGTGCACAGC 61.030 63.158 20.43 10.96 0.00 4.40
1963 1977 1.374758 GGAGGAAGACGGTGCACAG 60.375 63.158 20.43 18.06 0.00 3.66
2162 2176 1.135972 CAAACTTCTCCATGAACGCCG 60.136 52.381 0.00 0.00 0.00 6.46
2255 2269 2.919570 CGTACGTACGTTTCATCACG 57.080 50.000 33.95 23.51 44.13 4.35
2293 2307 2.935849 ACCACACACGTATGCATACATG 59.064 45.455 30.83 28.78 37.04 3.21
2351 2367 3.444388 TGTACGCACACACACATATAGGA 59.556 43.478 0.00 0.00 0.00 2.94
2352 2368 3.776340 TGTACGCACACACACATATAGG 58.224 45.455 0.00 0.00 0.00 2.57
2353 2369 5.276820 CCAATGTACGCACACACACATATAG 60.277 44.000 0.00 0.00 37.54 1.31
2377 2393 1.226128 GTACACGTACGGCCTCGAC 60.226 63.158 21.06 4.85 40.11 4.20
2455 2471 1.014352 ACAACGTTTGGTGTCAGCTC 58.986 50.000 0.00 0.00 34.12 4.09
2456 2472 2.210116 CTACAACGTTTGGTGTCAGCT 58.790 47.619 0.00 0.00 34.12 4.24
2474 2490 0.451383 GCATTGTGTTGGCATCGCTA 59.549 50.000 10.19 3.48 0.00 4.26
2501 2517 2.143925 CTTGAGAAGGGGACGTTTGTC 58.856 52.381 0.00 0.00 44.72 3.18
2504 2520 3.127425 CTTCTTGAGAAGGGGACGTTT 57.873 47.619 11.99 0.00 45.79 3.60
2514 2530 3.202906 CCAACGTTGACCTTCTTGAGAA 58.797 45.455 29.35 0.00 0.00 2.87
2515 2531 2.484770 CCCAACGTTGACCTTCTTGAGA 60.485 50.000 29.35 0.00 0.00 3.27
2516 2532 1.873591 CCCAACGTTGACCTTCTTGAG 59.126 52.381 29.35 8.26 0.00 3.02
2517 2533 1.487142 TCCCAACGTTGACCTTCTTGA 59.513 47.619 29.35 9.20 0.00 3.02
2518 2534 1.873591 CTCCCAACGTTGACCTTCTTG 59.126 52.381 29.35 9.71 0.00 3.02
2519 2535 1.489230 ACTCCCAACGTTGACCTTCTT 59.511 47.619 29.35 4.05 0.00 2.52
2520 2536 1.129058 ACTCCCAACGTTGACCTTCT 58.871 50.000 29.35 3.77 0.00 2.85
2521 2537 1.202604 TCACTCCCAACGTTGACCTTC 60.203 52.381 29.35 0.00 0.00 3.46
2522 2538 0.834612 TCACTCCCAACGTTGACCTT 59.165 50.000 29.35 8.15 0.00 3.50
2523 2539 0.393077 CTCACTCCCAACGTTGACCT 59.607 55.000 29.35 5.92 0.00 3.85
2524 2540 1.228657 GCTCACTCCCAACGTTGACC 61.229 60.000 29.35 4.59 0.00 4.02
2525 2541 1.228657 GGCTCACTCCCAACGTTGAC 61.229 60.000 29.35 0.00 0.00 3.18
2526 2542 1.070786 GGCTCACTCCCAACGTTGA 59.929 57.895 29.35 9.71 0.00 3.18
2527 2543 1.071471 AGGCTCACTCCCAACGTTG 59.929 57.895 21.47 21.47 0.00 4.10
2528 2544 1.071471 CAGGCTCACTCCCAACGTT 59.929 57.895 0.00 0.00 0.00 3.99
2529 2545 2.743718 CAGGCTCACTCCCAACGT 59.256 61.111 0.00 0.00 0.00 3.99
2530 2546 2.046892 CCAGGCTCACTCCCAACG 60.047 66.667 0.00 0.00 0.00 4.10
2531 2547 2.360475 GCCAGGCTCACTCCCAAC 60.360 66.667 3.29 0.00 0.00 3.77
2532 2548 2.530151 AGCCAGGCTCACTCCCAA 60.530 61.111 8.70 0.00 30.62 4.12
2541 2557 0.112995 TCAACCAATTGAGCCAGGCT 59.887 50.000 16.12 16.12 40.01 4.58
2542 2558 0.968405 TTCAACCAATTGAGCCAGGC 59.032 50.000 7.12 1.84 45.54 4.85
2543 2559 1.547372 CCTTCAACCAATTGAGCCAGG 59.453 52.381 7.12 1.85 45.54 4.45
2544 2560 2.490903 CTCCTTCAACCAATTGAGCCAG 59.509 50.000 7.12 0.00 45.54 4.85
2545 2561 2.158475 ACTCCTTCAACCAATTGAGCCA 60.158 45.455 7.12 0.00 45.54 4.75
2546 2562 2.229784 CACTCCTTCAACCAATTGAGCC 59.770 50.000 7.12 0.00 45.54 4.70
2547 2563 2.229784 CCACTCCTTCAACCAATTGAGC 59.770 50.000 7.12 0.00 45.54 4.26
2548 2564 3.754965 TCCACTCCTTCAACCAATTGAG 58.245 45.455 7.12 0.00 45.54 3.02
2549 2565 3.874383 TCCACTCCTTCAACCAATTGA 57.126 42.857 7.12 0.00 43.28 2.57
2550 2566 3.828451 ACATCCACTCCTTCAACCAATTG 59.172 43.478 0.00 0.00 37.14 2.32
2551 2567 4.118168 ACATCCACTCCTTCAACCAATT 57.882 40.909 0.00 0.00 0.00 2.32
2552 2568 3.814504 ACATCCACTCCTTCAACCAAT 57.185 42.857 0.00 0.00 0.00 3.16
2553 2569 3.392947 TGTACATCCACTCCTTCAACCAA 59.607 43.478 0.00 0.00 0.00 3.67
2554 2570 2.976185 TGTACATCCACTCCTTCAACCA 59.024 45.455 0.00 0.00 0.00 3.67
2555 2571 3.695830 TGTACATCCACTCCTTCAACC 57.304 47.619 0.00 0.00 0.00 3.77
2556 2572 4.215613 GGTTTGTACATCCACTCCTTCAAC 59.784 45.833 0.00 0.00 0.00 3.18
2557 2573 4.394729 GGTTTGTACATCCACTCCTTCAA 58.605 43.478 0.00 0.00 0.00 2.69
2558 2574 3.244770 GGGTTTGTACATCCACTCCTTCA 60.245 47.826 16.09 0.00 0.00 3.02
2559 2575 3.244770 TGGGTTTGTACATCCACTCCTTC 60.245 47.826 16.09 2.17 0.00 3.46
2560 2576 2.714250 TGGGTTTGTACATCCACTCCTT 59.286 45.455 16.09 0.00 0.00 3.36
2561 2577 2.344592 TGGGTTTGTACATCCACTCCT 58.655 47.619 16.09 0.00 0.00 3.69
2562 2578 2.817844 GTTGGGTTTGTACATCCACTCC 59.182 50.000 16.09 9.13 0.00 3.85
2563 2579 2.482721 CGTTGGGTTTGTACATCCACTC 59.517 50.000 16.09 6.61 0.00 3.51
2564 2580 2.158726 ACGTTGGGTTTGTACATCCACT 60.159 45.455 16.09 1.43 0.00 4.00
2565 2581 2.223745 ACGTTGGGTTTGTACATCCAC 58.776 47.619 16.09 6.03 0.00 4.02
2566 2582 2.105134 AGACGTTGGGTTTGTACATCCA 59.895 45.455 16.09 12.45 0.00 3.41
2567 2583 2.740447 GAGACGTTGGGTTTGTACATCC 59.260 50.000 0.00 2.58 0.00 3.51
2568 2584 2.410730 CGAGACGTTGGGTTTGTACATC 59.589 50.000 0.00 0.00 0.00 3.06
2569 2585 2.409975 CGAGACGTTGGGTTTGTACAT 58.590 47.619 0.00 0.00 0.00 2.29
2570 2586 1.538634 CCGAGACGTTGGGTTTGTACA 60.539 52.381 0.00 0.00 0.00 2.90
2571 2587 1.142474 CCGAGACGTTGGGTTTGTAC 58.858 55.000 0.00 0.00 0.00 2.90
2572 2588 0.752054 ACCGAGACGTTGGGTTTGTA 59.248 50.000 7.26 0.00 33.55 2.41
2573 2589 0.107557 AACCGAGACGTTGGGTTTGT 60.108 50.000 11.62 0.00 44.52 2.83
2574 2590 0.584876 GAACCGAGACGTTGGGTTTG 59.415 55.000 16.64 0.00 46.54 2.93
2575 2591 0.178533 TGAACCGAGACGTTGGGTTT 59.821 50.000 16.64 4.84 46.54 3.27
2577 2593 0.178533 TTTGAACCGAGACGTTGGGT 59.821 50.000 7.26 4.17 39.96 4.51
2578 2594 1.463444 GATTTGAACCGAGACGTTGGG 59.537 52.381 7.26 3.58 0.00 4.12
2579 2595 1.463444 GGATTTGAACCGAGACGTTGG 59.537 52.381 0.00 0.00 0.00 3.77
2580 2596 2.412089 GAGGATTTGAACCGAGACGTTG 59.588 50.000 0.00 0.00 0.00 4.10
2581 2597 2.036733 TGAGGATTTGAACCGAGACGTT 59.963 45.455 0.00 0.00 0.00 3.99
2582 2598 1.616865 TGAGGATTTGAACCGAGACGT 59.383 47.619 0.00 0.00 0.00 4.34
2583 2599 1.993370 GTGAGGATTTGAACCGAGACG 59.007 52.381 0.00 0.00 0.00 4.18
2584 2600 1.993370 CGTGAGGATTTGAACCGAGAC 59.007 52.381 0.00 0.00 0.00 3.36
2585 2601 2.363788 CGTGAGGATTTGAACCGAGA 57.636 50.000 0.00 0.00 0.00 4.04
2599 2615 0.249489 CCTAAATCCGCCTCCGTGAG 60.249 60.000 0.00 0.00 0.00 3.51
2600 2616 0.974010 ACCTAAATCCGCCTCCGTGA 60.974 55.000 0.00 0.00 0.00 4.35
2601 2617 0.107848 AACCTAAATCCGCCTCCGTG 60.108 55.000 0.00 0.00 0.00 4.94
2602 2618 0.616891 AAACCTAAATCCGCCTCCGT 59.383 50.000 0.00 0.00 0.00 4.69
2603 2619 1.134491 AGAAACCTAAATCCGCCTCCG 60.134 52.381 0.00 0.00 0.00 4.63
2604 2620 2.711978 AGAAACCTAAATCCGCCTCC 57.288 50.000 0.00 0.00 0.00 4.30
2605 2621 4.704965 ACATAGAAACCTAAATCCGCCTC 58.295 43.478 0.00 0.00 0.00 4.70
2606 2622 4.772886 ACATAGAAACCTAAATCCGCCT 57.227 40.909 0.00 0.00 0.00 5.52
2607 2623 4.036380 CCAACATAGAAACCTAAATCCGCC 59.964 45.833 0.00 0.00 0.00 6.13
2608 2624 4.638865 ACCAACATAGAAACCTAAATCCGC 59.361 41.667 0.00 0.00 0.00 5.54
2609 2625 5.448632 GCACCAACATAGAAACCTAAATCCG 60.449 44.000 0.00 0.00 0.00 4.18
2610 2626 5.417580 TGCACCAACATAGAAACCTAAATCC 59.582 40.000 0.00 0.00 0.00 3.01
2611 2627 6.374333 TCTGCACCAACATAGAAACCTAAATC 59.626 38.462 0.00 0.00 0.00 2.17
2612 2628 6.245408 TCTGCACCAACATAGAAACCTAAAT 58.755 36.000 0.00 0.00 0.00 1.40
2613 2629 5.626142 TCTGCACCAACATAGAAACCTAAA 58.374 37.500 0.00 0.00 0.00 1.85
2614 2630 5.235850 TCTGCACCAACATAGAAACCTAA 57.764 39.130 0.00 0.00 0.00 2.69
2615 2631 4.323485 CCTCTGCACCAACATAGAAACCTA 60.323 45.833 0.00 0.00 0.00 3.08
2616 2632 3.560025 CCTCTGCACCAACATAGAAACCT 60.560 47.826 0.00 0.00 0.00 3.50
2617 2633 2.749621 CCTCTGCACCAACATAGAAACC 59.250 50.000 0.00 0.00 0.00 3.27
2618 2634 2.162408 GCCTCTGCACCAACATAGAAAC 59.838 50.000 0.00 0.00 37.47 2.78
2619 2635 2.040278 AGCCTCTGCACCAACATAGAAA 59.960 45.455 0.00 0.00 41.13 2.52
2620 2636 1.630369 AGCCTCTGCACCAACATAGAA 59.370 47.619 0.00 0.00 41.13 2.10
2621 2637 1.065926 CAGCCTCTGCACCAACATAGA 60.066 52.381 0.00 0.00 41.13 1.98
2622 2638 1.065926 TCAGCCTCTGCACCAACATAG 60.066 52.381 0.00 0.00 41.13 2.23
2623 2639 0.983467 TCAGCCTCTGCACCAACATA 59.017 50.000 0.00 0.00 41.13 2.29
2624 2640 0.322277 CTCAGCCTCTGCACCAACAT 60.322 55.000 0.00 0.00 41.13 2.71
2625 2641 1.071987 CTCAGCCTCTGCACCAACA 59.928 57.895 0.00 0.00 41.13 3.33
2626 2642 0.673022 CTCTCAGCCTCTGCACCAAC 60.673 60.000 0.00 0.00 41.13 3.77
2627 2643 0.833409 TCTCTCAGCCTCTGCACCAA 60.833 55.000 0.00 0.00 41.13 3.67
2628 2644 1.228988 TCTCTCAGCCTCTGCACCA 60.229 57.895 0.00 0.00 41.13 4.17
2629 2645 1.516892 CTCTCTCAGCCTCTGCACC 59.483 63.158 0.00 0.00 41.13 5.01
2630 2646 1.153588 GCTCTCTCAGCCTCTGCAC 60.154 63.158 0.00 0.00 43.17 4.57
2631 2647 2.708865 CGCTCTCTCAGCCTCTGCA 61.709 63.158 0.00 0.00 46.74 4.41
2632 2648 2.104729 CGCTCTCTCAGCCTCTGC 59.895 66.667 0.00 0.00 46.74 4.26
2633 2649 2.806929 CCGCTCTCTCAGCCTCTG 59.193 66.667 0.00 0.00 46.74 3.35
2634 2650 3.146913 GCCGCTCTCTCAGCCTCT 61.147 66.667 0.00 0.00 46.74 3.69
2635 2651 4.567385 CGCCGCTCTCTCAGCCTC 62.567 72.222 0.00 0.00 46.74 4.70
2655 2671 1.976474 TGTGAGGGGCAAAATCCGC 60.976 57.895 0.00 0.00 39.15 5.54
2656 2672 0.609131 AGTGTGAGGGGCAAAATCCG 60.609 55.000 0.00 0.00 0.00 4.18
2657 2673 0.890683 CAGTGTGAGGGGCAAAATCC 59.109 55.000 0.00 0.00 0.00 3.01
2658 2674 1.620822 ACAGTGTGAGGGGCAAAATC 58.379 50.000 0.00 0.00 0.00 2.17
2659 2675 2.086610 AACAGTGTGAGGGGCAAAAT 57.913 45.000 0.00 0.00 0.00 1.82
2660 2676 2.738587 TAACAGTGTGAGGGGCAAAA 57.261 45.000 0.00 0.00 0.00 2.44
2661 2677 2.969821 ATAACAGTGTGAGGGGCAAA 57.030 45.000 0.00 0.00 0.00 3.68
2662 2678 2.026636 GGTATAACAGTGTGAGGGGCAA 60.027 50.000 0.00 0.00 0.00 4.52
2663 2679 1.557832 GGTATAACAGTGTGAGGGGCA 59.442 52.381 0.00 0.00 0.00 5.36
2664 2680 1.838077 AGGTATAACAGTGTGAGGGGC 59.162 52.381 0.00 0.00 0.00 5.80
2665 2681 3.430374 CGAAGGTATAACAGTGTGAGGGG 60.430 52.174 0.00 0.00 0.00 4.79
2666 2682 3.194968 ACGAAGGTATAACAGTGTGAGGG 59.805 47.826 0.00 0.00 0.00 4.30
2667 2683 4.451629 ACGAAGGTATAACAGTGTGAGG 57.548 45.455 0.00 0.00 0.00 3.86
2668 2684 5.510674 CGTAACGAAGGTATAACAGTGTGAG 59.489 44.000 0.00 0.00 0.00 3.51
2669 2685 5.181056 TCGTAACGAAGGTATAACAGTGTGA 59.819 40.000 0.00 0.00 31.06 3.58
2670 2686 5.284660 GTCGTAACGAAGGTATAACAGTGTG 59.715 44.000 0.00 0.00 37.72 3.82
2671 2687 5.393962 GTCGTAACGAAGGTATAACAGTGT 58.606 41.667 0.00 0.00 37.72 3.55
2672 2688 5.921784 GTCGTAACGAAGGTATAACAGTG 57.078 43.478 0.00 0.00 37.72 3.66
2687 2703 4.125097 CGCCGCCAACGTCGTAAC 62.125 66.667 0.00 0.00 35.65 2.50
2705 2721 0.449388 CACGGATCAAAGCAAGGAGC 59.551 55.000 0.00 0.00 46.19 4.70
2706 2722 0.449388 GCACGGATCAAAGCAAGGAG 59.551 55.000 0.00 0.00 0.00 3.69
2707 2723 1.298157 CGCACGGATCAAAGCAAGGA 61.298 55.000 0.00 0.00 0.00 3.36
2708 2724 1.135315 CGCACGGATCAAAGCAAGG 59.865 57.895 0.00 0.00 0.00 3.61
2709 2725 1.512734 GCGCACGGATCAAAGCAAG 60.513 57.895 0.30 0.00 0.00 4.01
2710 2726 1.965930 AGCGCACGGATCAAAGCAA 60.966 52.632 11.47 0.00 0.00 3.91
2791 2807 2.659016 CAGAGAGAAGCGGGCACA 59.341 61.111 0.00 0.00 0.00 4.57
2801 2817 2.429767 CCCGCATCTGGCAGAGAGA 61.430 63.158 23.24 0.00 45.17 3.10
2824 2840 3.682292 GAGATCCACGGCCACCACC 62.682 68.421 2.24 0.00 0.00 4.61
2834 2850 0.241481 GGACGATAGCCGAGATCCAC 59.759 60.000 0.00 0.00 41.76 4.02
2845 2861 4.537965 CCGTTGTAAGATCTGGACGATAG 58.462 47.826 16.94 8.39 46.19 2.08
2860 2876 2.262292 GCCACCGTAGCCGTTGTA 59.738 61.111 0.00 0.00 0.00 2.41
2910 2926 2.829914 CCATCCGCACCACCATGG 60.830 66.667 11.19 11.19 45.02 3.66
2922 2938 4.828296 CCTGGCTGGCCACCATCC 62.828 72.222 22.35 12.90 41.89 3.51
2976 2992 3.063997 GCCATCACCTTTATTCACGACAG 59.936 47.826 0.00 0.00 0.00 3.51
2979 2995 2.639065 GGCCATCACCTTTATTCACGA 58.361 47.619 0.00 0.00 0.00 4.35
2981 2997 2.952310 GAGGGCCATCACCTTTATTCAC 59.048 50.000 13.69 0.00 38.79 3.18
2994 3010 3.064324 GCAAAGCACGAGGGCCAT 61.064 61.111 6.18 0.00 0.00 4.40
2995 3011 4.269523 AGCAAAGCACGAGGGCCA 62.270 61.111 6.18 0.00 0.00 5.36
2998 3014 3.793144 GCGAGCAAAGCACGAGGG 61.793 66.667 12.68 0.00 44.57 4.30
3013 3029 3.918220 GAGCGTTGCCGAGATGCG 61.918 66.667 0.00 0.00 40.47 4.73
3022 3038 1.980951 TTGATCATGCCGAGCGTTGC 61.981 55.000 0.00 0.00 30.45 4.17
3028 3044 1.134580 AGGAGTGTTGATCATGCCGAG 60.135 52.381 0.00 0.00 0.00 4.63
3040 3056 3.368843 CGATGACCAGATCAAGGAGTGTT 60.369 47.826 10.82 0.00 41.93 3.32
3041 3057 2.167281 CGATGACCAGATCAAGGAGTGT 59.833 50.000 10.82 0.00 41.93 3.55
3043 3059 2.428890 GTCGATGACCAGATCAAGGAGT 59.571 50.000 10.82 0.00 41.93 3.85
3083 3099 0.755079 TCTCCTGGGCAAGATCATCG 59.245 55.000 0.00 0.00 0.00 3.84
3085 3101 2.372504 CAGATCTCCTGGGCAAGATCAT 59.627 50.000 20.02 7.76 46.79 2.45
3096 3112 3.696045 ACTATCCGATCCAGATCTCCTG 58.304 50.000 6.12 0.00 42.55 3.86
3111 3127 1.080025 GCACGGCCGGATACTATCC 60.080 63.158 31.76 5.10 46.22 2.59
3114 3130 2.809706 GTGCACGGCCGGATACTA 59.190 61.111 31.76 6.38 0.00 1.82
3116 3132 4.807039 ACGTGCACGGCCGGATAC 62.807 66.667 39.21 22.15 44.95 2.24
3124 3140 0.385473 GTTGATTTGGACGTGCACGG 60.385 55.000 39.21 23.04 44.95 4.94
3130 3146 2.353406 CCTCGTAGGTTGATTTGGACGT 60.353 50.000 0.00 0.00 0.00 4.34
3148 3164 2.125350 CTGCGCCCTCAGAACCTC 60.125 66.667 4.18 0.00 36.19 3.85
3173 3189 5.526111 CCCATGGTATTAACAAACTACGGAG 59.474 44.000 11.73 0.00 0.00 4.63
3176 3192 5.875910 TGTCCCATGGTATTAACAAACTACG 59.124 40.000 11.73 0.00 0.00 3.51
3177 3193 7.875327 ATGTCCCATGGTATTAACAAACTAC 57.125 36.000 11.73 0.00 0.00 2.73
3187 3203 4.448431 AGGCCTATATGTCCCATGGTATT 58.552 43.478 1.29 0.00 0.00 1.89
3202 3218 3.648067 TCCATGAAAATCGAGAGGCCTAT 59.352 43.478 4.42 0.00 0.00 2.57
3204 3220 1.839994 TCCATGAAAATCGAGAGGCCT 59.160 47.619 3.86 3.86 0.00 5.19
3217 3233 5.594317 TCTTCATCGATGTCTACTCCATGAA 59.406 40.000 24.09 7.32 0.00 2.57
3218 3234 5.133221 TCTTCATCGATGTCTACTCCATGA 58.867 41.667 24.09 7.90 0.00 3.07


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

AutoCloner maintained by Alex Coulton.