Multiple sequence alignment - TraesCS7A01G414300

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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 TraesCS7A01G414300 chr7A 100.000 2901 0 0 1 2901 604854949 604852049 0.000000e+00 5358.0
1 TraesCS7A01G414300 chr7B 90.413 1815 97 29 523 2309 561281328 561279563 0.000000e+00 2316.0
2 TraesCS7A01G414300 chr7B 82.997 347 36 14 2315 2642 561278932 561278590 2.830000e-75 292.0
3 TraesCS7A01G414300 chr7D 91.162 1618 56 29 523 2127 524916552 524915009 0.000000e+00 2115.0
4 TraesCS7A01G414300 chr7D 95.951 494 17 2 2125 2617 524913140 524912649 0.000000e+00 798.0
5 TraesCS7A01G414300 chr7D 100.000 30 0 0 2614 2643 524901032 524901003 4.040000e-04 56.5
6 TraesCS7A01G414300 chr1A 95.611 524 21 2 1 523 48781962 48782484 0.000000e+00 839.0
7 TraesCS7A01G414300 chr1A 95.411 523 23 1 1 522 515580941 515581463 0.000000e+00 832.0
8 TraesCS7A01G414300 chr1A 86.486 222 30 0 1212 1433 551592921 551592700 8.030000e-61 244.0
9 TraesCS7A01G414300 chr1A 93.902 82 5 0 1349 1430 444136846 444136927 1.090000e-24 124.0
10 TraesCS7A01G414300 chr1A 82.979 141 9 7 2641 2778 483657406 483657278 2.360000e-21 113.0
11 TraesCS7A01G414300 chr5A 95.229 524 21 1 3 522 331381563 331382086 0.000000e+00 826.0
12 TraesCS7A01G414300 chr5A 95.057 526 25 1 1 525 675642853 675642328 0.000000e+00 826.0
13 TraesCS7A01G414300 chr5A 94.886 528 25 2 1 527 645986045 645986571 0.000000e+00 824.0
14 TraesCS7A01G414300 chr5A 86.667 210 28 0 1219 1428 436089395 436089604 1.740000e-57 233.0
15 TraesCS7A01G414300 chr3A 94.896 529 22 2 2 526 536884580 536885107 0.000000e+00 822.0
16 TraesCS7A01G414300 chr3A 94.847 524 26 1 1 523 169080259 169079736 0.000000e+00 817.0
17 TraesCS7A01G414300 chr3A 85.950 121 6 5 2638 2758 114612565 114612674 5.080000e-23 119.0
18 TraesCS7A01G414300 chr3A 85.246 122 7 3 2637 2758 711380233 711380123 6.570000e-22 115.0
19 TraesCS7A01G414300 chr4A 94.847 524 25 2 1 523 72002744 72002222 0.000000e+00 817.0
20 TraesCS7A01G414300 chr4A 85.366 123 11 3 2637 2758 571041268 571041384 1.410000e-23 121.0
21 TraesCS7A01G414300 chr4A 84.800 125 7 5 2634 2758 431021246 431021134 6.570000e-22 115.0
22 TraesCS7A01G414300 chr6A 94.615 520 27 1 4 523 579394705 579394187 0.000000e+00 804.0
23 TraesCS7A01G414300 chr6A 85.833 120 6 3 2640 2759 394506214 394506106 1.830000e-22 117.0
24 TraesCS7A01G414300 chr6A 85.714 119 6 5 2641 2759 309871486 309871593 6.570000e-22 115.0
25 TraesCS7A01G414300 chr1D 77.483 453 75 21 1001 1433 459880642 459880197 2.230000e-61 246.0
26 TraesCS7A01G414300 chr1B 86.977 215 28 0 1219 1433 631967501 631967287 2.890000e-60 243.0
27 TraesCS7A01G414300 chr5D 85.714 210 30 0 1219 1428 334255464 334255673 3.760000e-54 222.0
28 TraesCS7A01G414300 chr5B 85.714 210 30 0 1219 1428 391144957 391145166 3.760000e-54 222.0
29 TraesCS7A01G414300 chrUn 86.777 121 5 3 2638 2758 362393452 362393343 1.090000e-24 124.0
30 TraesCS7A01G414300 chr3B 84.252 127 9 5 2632 2758 806722538 806722653 2.360000e-21 113.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G414300 chr7A 604852049 604854949 2900 True 5358.0 5358 100.0000 1 2901 1 chr7A.!!$R1 2900
1 TraesCS7A01G414300 chr7B 561278590 561281328 2738 True 1304.0 2316 86.7050 523 2642 2 chr7B.!!$R1 2119
2 TraesCS7A01G414300 chr7D 524912649 524916552 3903 True 1456.5 2115 93.5565 523 2617 2 chr7D.!!$R2 2094
3 TraesCS7A01G414300 chr1A 48781962 48782484 522 False 839.0 839 95.6110 1 523 1 chr1A.!!$F1 522
4 TraesCS7A01G414300 chr1A 515580941 515581463 522 False 832.0 832 95.4110 1 522 1 chr1A.!!$F3 521
5 TraesCS7A01G414300 chr5A 331381563 331382086 523 False 826.0 826 95.2290 3 522 1 chr5A.!!$F1 519
6 TraesCS7A01G414300 chr5A 675642328 675642853 525 True 826.0 826 95.0570 1 525 1 chr5A.!!$R1 524
7 TraesCS7A01G414300 chr5A 645986045 645986571 526 False 824.0 824 94.8860 1 527 1 chr5A.!!$F3 526
8 TraesCS7A01G414300 chr3A 536884580 536885107 527 False 822.0 822 94.8960 2 526 1 chr3A.!!$F2 524
9 TraesCS7A01G414300 chr3A 169079736 169080259 523 True 817.0 817 94.8470 1 523 1 chr3A.!!$R1 522
10 TraesCS7A01G414300 chr4A 72002222 72002744 522 True 817.0 817 94.8470 1 523 1 chr4A.!!$R1 522
11 TraesCS7A01G414300 chr6A 579394187 579394705 518 True 804.0 804 94.6150 4 523 1 chr6A.!!$R2 519

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
762 771 0.478507 GAGAGAGAGAGGGAGGGAGG 59.521 65.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2741 5316 0.115745 AGGTACTCCCTCCGTTCCAA 59.884 55.0 0.0 0.0 40.71 3.53 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
173 174 3.469970 TGGCGGCCATGTCGAGAT 61.470 61.111 19.77 0.00 29.41 2.75
232 236 4.280494 GCGGCCGGAGAATAGCGA 62.280 66.667 29.38 0.00 0.00 4.93
342 351 4.717629 CAAGGGCGTGCGTCGAGA 62.718 66.667 0.00 0.00 42.86 4.04
413 422 2.552585 GATGGGTCGAAAGCGGACGA 62.553 60.000 0.00 0.00 38.28 4.20
505 514 1.335132 GGGCGAACAGGATAGGGTGA 61.335 60.000 0.00 0.00 0.00 4.02
510 519 0.968901 AACAGGATAGGGTGACGCGA 60.969 55.000 15.93 0.00 0.00 5.87
538 547 1.451567 CCTGAGGGACATGCTGCAG 60.452 63.158 10.11 10.11 33.58 4.41
631 640 2.971901 ACCCCTTCCTAGTTGTTTGG 57.028 50.000 0.00 0.00 0.00 3.28
635 644 1.545841 CTTCCTAGTTGTTTGGGCCC 58.454 55.000 17.59 17.59 0.00 5.80
654 663 1.432514 CTGTCCGTGTGTGAGATTGG 58.567 55.000 0.00 0.00 0.00 3.16
689 698 3.588955 TGAAACGATGGATGACAGACAG 58.411 45.455 0.00 0.00 0.00 3.51
691 700 2.662006 ACGATGGATGACAGACAGTG 57.338 50.000 0.00 0.00 0.00 3.66
709 718 1.211457 GTGCAAGGGAGAGATGGATGT 59.789 52.381 0.00 0.00 0.00 3.06
713 722 2.770802 CAAGGGAGAGATGGATGTCACT 59.229 50.000 0.00 0.00 0.00 3.41
714 723 2.396608 AGGGAGAGATGGATGTCACTG 58.603 52.381 0.00 0.00 0.00 3.66
716 725 2.102252 GGGAGAGATGGATGTCACTGTC 59.898 54.545 0.00 0.00 0.00 3.51
717 726 2.762887 GGAGAGATGGATGTCACTGTCA 59.237 50.000 0.00 0.00 0.00 3.58
718 727 3.430098 GGAGAGATGGATGTCACTGTCAC 60.430 52.174 0.00 0.00 0.00 3.67
719 728 3.439154 AGAGATGGATGTCACTGTCACT 58.561 45.455 0.00 0.00 0.00 3.41
720 729 3.195182 AGAGATGGATGTCACTGTCACTG 59.805 47.826 0.00 0.00 0.00 3.66
721 730 2.005451 GATGGATGTCACTGTCACTGC 58.995 52.381 0.00 0.00 0.00 4.40
724 733 1.339438 GGATGTCACTGTCACTGCCAT 60.339 52.381 0.00 0.00 0.00 4.40
754 763 2.224329 CCATTGCCATGAGAGAGAGAGG 60.224 54.545 0.00 0.00 31.07 3.69
762 771 0.478507 GAGAGAGAGAGGGAGGGAGG 59.521 65.000 0.00 0.00 0.00 4.30
764 773 0.996762 GAGAGAGAGGGAGGGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
769 778 0.556380 AGAGGGAGGGAGGGAGAGAA 60.556 60.000 0.00 0.00 0.00 2.87
879 891 3.877508 GGCCGCATTATATATCTCCAACC 59.122 47.826 0.00 0.00 0.00 3.77
943 955 2.609339 TCCCATCCGGAGCTAGCT 59.391 61.111 19.45 19.45 34.86 3.32
944 956 1.834378 TCCCATCCGGAGCTAGCTG 60.834 63.158 24.99 8.72 34.86 4.24
945 957 2.739784 CCATCCGGAGCTAGCTGG 59.260 66.667 24.99 18.49 35.54 4.85
980 1006 0.899019 ACTCGAGGAAGAAAGGAGCC 59.101 55.000 18.41 0.00 0.00 4.70
1011 1037 0.748367 GGGAGAAAATGGGTCGAGCC 60.748 60.000 26.70 26.70 0.00 4.70
1154 1180 3.801293 GCCGGTATGTCCATTACACCTAC 60.801 52.174 1.90 0.00 42.09 3.18
1222 1255 1.134699 TGTCGTGGAGATGATTCAGGC 60.135 52.381 0.00 0.00 0.00 4.85
1303 1336 2.202492 CACGGCGACTTCTCCGAG 60.202 66.667 16.62 2.72 46.30 4.63
1487 1520 2.230653 ACCCATGGCCAGCAGTACA 61.231 57.895 13.05 0.00 0.00 2.90
1495 1528 1.892819 GCCAGCAGTACAGCTCCAGA 61.893 60.000 10.18 0.00 44.54 3.86
1523 1556 1.303091 ACCGCCATTTACCGTTGAGC 61.303 55.000 0.00 0.00 0.00 4.26
1524 1557 1.302383 CCGCCATTTACCGTTGAGCA 61.302 55.000 0.00 0.00 0.00 4.26
1525 1558 0.179200 CGCCATTTACCGTTGAGCAC 60.179 55.000 0.00 0.00 0.00 4.40
1546 1588 1.204941 CACCACCACACTAGCTCTACC 59.795 57.143 0.00 0.00 0.00 3.18
1628 1679 0.456142 GCAGCAGTACATGTCGTCGA 60.456 55.000 0.00 0.00 0.00 4.20
1673 1724 3.738246 CCAGTGCTGCTGCTGCTG 61.738 66.667 27.67 23.17 43.71 4.41
1752 1803 0.322975 CAGGAGGAGGACACCAACAG 59.677 60.000 0.00 0.00 0.00 3.16
1759 1810 1.968540 GGACACCAACAGCCTGCTC 60.969 63.158 0.00 0.00 0.00 4.26
1829 1883 0.175531 TGAGATGATTTCGCCGAGCA 59.824 50.000 0.00 0.00 0.00 4.26
1970 2024 8.444715 TGATGTTAATTTCTTTGCATGCATTTC 58.555 29.630 23.37 6.57 0.00 2.17
1991 2046 2.067605 CCCGGCCGCCCCATATATA 61.068 63.158 22.85 0.00 0.00 0.86
1992 2047 1.445942 CCGGCCGCCCCATATATAG 59.554 63.158 22.85 0.00 0.00 1.31
1995 2050 0.759346 GGCCGCCCCATATATAGGAG 59.241 60.000 0.00 0.00 0.00 3.69
2036 2091 4.699637 CCGATGCAGGTTGGTTAGTATTA 58.300 43.478 0.00 0.00 0.00 0.98
2040 2095 7.442969 CCGATGCAGGTTGGTTAGTATTATTTA 59.557 37.037 0.00 0.00 0.00 1.40
2093 2148 3.329520 GAGATGACCTCTCCCTAGCTAGA 59.670 52.174 22.70 2.75 44.06 2.43
2222 4148 7.802738 TCATGGAACTAAACATTCGTTTGTAG 58.197 34.615 0.95 0.00 45.01 2.74
2312 4869 5.319453 TGCGCTAATATACTACACCTAGGT 58.681 41.667 9.21 9.21 0.00 3.08
2313 4870 6.475504 TGCGCTAATATACTACACCTAGGTA 58.524 40.000 15.80 0.00 0.00 3.08
2369 4926 9.534565 ACAGTACACTAACATGAATGCTTATAG 57.465 33.333 0.00 0.00 0.00 1.31
2436 4993 0.111134 GTAACGCCGAACCGTCAAAC 60.111 55.000 0.00 0.00 41.16 2.93
2460 5017 6.271159 ACTTTAACTCCTCAAACATCTCCTCT 59.729 38.462 0.00 0.00 0.00 3.69
2474 5031 8.785329 AACATCTCCTCTAATCTTCACTTTTC 57.215 34.615 0.00 0.00 0.00 2.29
2522 5082 3.121738 ACCTAACAGAACCCTCAAACG 57.878 47.619 0.00 0.00 0.00 3.60
2533 5093 1.066358 CCCTCAAACGAACTAGACCCC 60.066 57.143 0.00 0.00 0.00 4.95
2539 5099 0.902531 ACGAACTAGACCCCACATGG 59.097 55.000 0.00 0.00 0.00 3.66
2547 5119 0.035056 GACCCCACATGGAACCTCTG 60.035 60.000 0.00 0.00 37.39 3.35
2559 5131 2.290387 GGAACCTCTGTCTCCCTTTTCC 60.290 54.545 0.00 0.00 0.00 3.13
2569 5141 4.599241 TGTCTCCCTTTTCCTCATTCTTCT 59.401 41.667 0.00 0.00 0.00 2.85
2614 5189 1.135972 CCAACGATGACTTTTCGGCAG 60.136 52.381 0.00 0.00 40.83 4.85
2625 5200 5.122239 TGACTTTTCGGCAGTAGATGATTTG 59.878 40.000 0.00 0.00 0.00 2.32
2637 5212 1.266175 GATGATTTGCATGCGCTAGCT 59.734 47.619 21.66 5.57 45.42 3.32
2642 5217 1.852942 TTGCATGCGCTAGCTAGTAC 58.147 50.000 21.62 14.19 45.42 2.73
2643 5218 1.032794 TGCATGCGCTAGCTAGTACT 58.967 50.000 21.62 0.00 45.42 2.73
2644 5219 1.001268 TGCATGCGCTAGCTAGTACTC 60.001 52.381 21.62 9.15 45.42 2.59
2645 5220 1.667467 GCATGCGCTAGCTAGTACTCC 60.667 57.143 21.62 4.06 45.42 3.85
2646 5221 1.068194 CATGCGCTAGCTAGTACTCCC 60.068 57.143 21.62 3.35 45.42 4.30
2647 5222 0.183014 TGCGCTAGCTAGTACTCCCT 59.817 55.000 21.62 0.00 45.42 4.20
2648 5223 0.876399 GCGCTAGCTAGTACTCCCTC 59.124 60.000 21.62 1.92 41.01 4.30
2649 5224 1.525941 CGCTAGCTAGTACTCCCTCC 58.474 60.000 21.62 1.21 0.00 4.30
2650 5225 1.525941 GCTAGCTAGTACTCCCTCCG 58.474 60.000 21.62 0.00 0.00 4.63
2651 5226 1.202794 GCTAGCTAGTACTCCCTCCGT 60.203 57.143 21.62 0.00 0.00 4.69
2652 5227 2.749132 GCTAGCTAGTACTCCCTCCGTT 60.749 54.545 21.62 0.00 0.00 4.44
2653 5228 2.055684 AGCTAGTACTCCCTCCGTTC 57.944 55.000 0.00 0.00 0.00 3.95
2654 5229 1.031235 GCTAGTACTCCCTCCGTTCC 58.969 60.000 0.00 0.00 0.00 3.62
2655 5230 1.684248 GCTAGTACTCCCTCCGTTCCA 60.684 57.143 0.00 0.00 0.00 3.53
2656 5231 2.731572 CTAGTACTCCCTCCGTTCCAA 58.268 52.381 0.00 0.00 0.00 3.53
2657 5232 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2658 5233 2.547990 AGTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
2659 5234 2.910977 AGTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
2660 5235 4.098894 AGTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
2661 5236 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2662 5237 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2663 5238 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2664 5239 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2665 5240 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2666 5241 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2667 5242 3.368116 CCTCCGTTCCAAATTACTCGTCT 60.368 47.826 0.00 0.00 0.00 4.18
2668 5243 3.841643 TCCGTTCCAAATTACTCGTCTC 58.158 45.455 0.00 0.00 0.00 3.36
2669 5244 3.256383 TCCGTTCCAAATTACTCGTCTCA 59.744 43.478 0.00 0.00 0.00 3.27
2670 5245 3.612860 CCGTTCCAAATTACTCGTCTCAG 59.387 47.826 0.00 0.00 0.00 3.35
2671 5246 4.482386 CGTTCCAAATTACTCGTCTCAGA 58.518 43.478 0.00 0.00 0.00 3.27
2672 5247 4.921515 CGTTCCAAATTACTCGTCTCAGAA 59.078 41.667 0.00 0.00 0.00 3.02
2673 5248 5.404366 CGTTCCAAATTACTCGTCTCAGAAA 59.596 40.000 0.00 0.00 0.00 2.52
2674 5249 6.090898 CGTTCCAAATTACTCGTCTCAGAAAT 59.909 38.462 0.00 0.00 0.00 2.17
2675 5250 7.274904 CGTTCCAAATTACTCGTCTCAGAAATA 59.725 37.037 0.00 0.00 0.00 1.40
2676 5251 8.932791 GTTCCAAATTACTCGTCTCAGAAATAA 58.067 33.333 0.00 0.00 0.00 1.40
2677 5252 9.496873 TTCCAAATTACTCGTCTCAGAAATAAA 57.503 29.630 0.00 0.00 0.00 1.40
2678 5253 9.496873 TCCAAATTACTCGTCTCAGAAATAAAA 57.503 29.630 0.00 0.00 0.00 1.52
2686 5261 9.877178 ACTCGTCTCAGAAATAAAAATAGATGT 57.123 29.630 0.00 0.00 0.00 3.06
2726 5301 7.561021 ACATCTAGATACATCTATACCTGCG 57.439 40.000 4.54 0.00 38.60 5.18
2727 5302 7.339482 ACATCTAGATACATCTATACCTGCGA 58.661 38.462 4.54 0.00 38.60 5.10
2728 5303 7.996066 ACATCTAGATACATCTATACCTGCGAT 59.004 37.037 4.54 0.00 38.60 4.58
2729 5304 9.495572 CATCTAGATACATCTATACCTGCGATA 57.504 37.037 4.54 0.00 38.60 2.92
2731 5306 9.549078 TCTAGATACATCTATACCTGCGATAAG 57.451 37.037 0.00 0.00 38.60 1.73
2732 5307 9.332502 CTAGATACATCTATACCTGCGATAAGT 57.667 37.037 0.00 0.00 38.60 2.24
2734 5309 9.682465 AGATACATCTATACCTGCGATAAGTAA 57.318 33.333 0.00 0.00 34.85 2.24
2737 5312 8.179509 ACATCTATACCTGCGATAAGTAAAGT 57.820 34.615 0.00 0.00 0.00 2.66
2738 5313 9.293404 ACATCTATACCTGCGATAAGTAAAGTA 57.707 33.333 0.00 0.00 0.00 2.24
2744 5319 7.316544 ACCTGCGATAAGTAAAGTAATTTGG 57.683 36.000 0.00 0.00 0.00 3.28
2745 5320 7.107542 ACCTGCGATAAGTAAAGTAATTTGGA 58.892 34.615 0.00 0.00 0.00 3.53
2746 5321 7.608761 ACCTGCGATAAGTAAAGTAATTTGGAA 59.391 33.333 0.00 0.00 0.00 3.53
2747 5322 7.908601 CCTGCGATAAGTAAAGTAATTTGGAAC 59.091 37.037 0.00 0.00 0.00 3.62
2748 5323 7.457868 TGCGATAAGTAAAGTAATTTGGAACG 58.542 34.615 0.00 0.00 0.00 3.95
2749 5324 6.903479 GCGATAAGTAAAGTAATTTGGAACGG 59.097 38.462 0.00 0.00 0.00 4.44
2750 5325 7.201548 GCGATAAGTAAAGTAATTTGGAACGGA 60.202 37.037 0.00 0.00 0.00 4.69
2751 5326 8.325997 CGATAAGTAAAGTAATTTGGAACGGAG 58.674 37.037 0.00 0.00 0.00 4.63
2752 5327 6.812879 AAGTAAAGTAATTTGGAACGGAGG 57.187 37.500 0.00 0.00 0.00 4.30
2753 5328 5.250982 AGTAAAGTAATTTGGAACGGAGGG 58.749 41.667 0.00 0.00 0.00 4.30
2754 5329 4.376225 AAAGTAATTTGGAACGGAGGGA 57.624 40.909 0.00 0.00 0.00 4.20
2755 5330 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
2756 5331 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
2757 5332 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
2758 5333 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
2759 5334 0.978907 TTTGGAACGGAGGGAGTACC 59.021 55.000 0.00 0.00 40.67 3.34
2774 5349 6.506538 GGGAGTACCTAGGGTATATATCGA 57.493 45.833 14.81 0.00 40.54 3.59
2775 5350 7.089106 GGGAGTACCTAGGGTATATATCGAT 57.911 44.000 14.81 2.16 40.54 3.59
2776 5351 6.941436 GGGAGTACCTAGGGTATATATCGATG 59.059 46.154 14.81 0.00 40.54 3.84
2777 5352 6.430616 GGAGTACCTAGGGTATATATCGATGC 59.569 46.154 14.81 0.00 40.54 3.91
2778 5353 7.151694 AGTACCTAGGGTATATATCGATGCT 57.848 40.000 14.81 0.00 40.54 3.79
2779 5354 7.225725 AGTACCTAGGGTATATATCGATGCTC 58.774 42.308 14.81 0.00 40.54 4.26
2780 5355 5.386924 ACCTAGGGTATATATCGATGCTCC 58.613 45.833 14.81 3.53 32.11 4.70
2781 5356 4.456222 CCTAGGGTATATATCGATGCTCCG 59.544 50.000 8.54 0.00 0.00 4.63
2782 5357 2.623889 AGGGTATATATCGATGCTCCGC 59.376 50.000 8.54 0.90 0.00 5.54
2783 5358 2.361119 GGGTATATATCGATGCTCCGCA 59.639 50.000 8.54 0.00 44.86 5.69
2784 5359 3.181479 GGGTATATATCGATGCTCCGCAA 60.181 47.826 8.54 0.00 43.62 4.85
2785 5360 4.430007 GGTATATATCGATGCTCCGCAAA 58.570 43.478 8.54 0.00 43.62 3.68
2786 5361 4.868171 GGTATATATCGATGCTCCGCAAAA 59.132 41.667 8.54 0.00 43.62 2.44
2787 5362 5.350365 GGTATATATCGATGCTCCGCAAAAA 59.650 40.000 8.54 0.00 43.62 1.94
2788 5363 3.609103 ATATCGATGCTCCGCAAAAAC 57.391 42.857 8.54 0.00 43.62 2.43
2789 5364 1.164411 ATCGATGCTCCGCAAAAACA 58.836 45.000 0.00 0.00 43.62 2.83
2790 5365 0.947960 TCGATGCTCCGCAAAAACAA 59.052 45.000 0.00 0.00 43.62 2.83
2791 5366 1.539388 TCGATGCTCCGCAAAAACAAT 59.461 42.857 0.00 0.00 43.62 2.71
2792 5367 2.744741 TCGATGCTCCGCAAAAACAATA 59.255 40.909 0.00 0.00 43.62 1.90
2793 5368 3.376859 TCGATGCTCCGCAAAAACAATAT 59.623 39.130 0.00 0.00 43.62 1.28
2794 5369 4.572795 TCGATGCTCCGCAAAAACAATATA 59.427 37.500 0.00 0.00 43.62 0.86
2795 5370 5.065346 TCGATGCTCCGCAAAAACAATATAA 59.935 36.000 0.00 0.00 43.62 0.98
2796 5371 5.171337 CGATGCTCCGCAAAAACAATATAAC 59.829 40.000 0.00 0.00 43.62 1.89
2797 5372 5.378292 TGCTCCGCAAAAACAATATAACA 57.622 34.783 0.00 0.00 34.76 2.41
2798 5373 5.398169 TGCTCCGCAAAAACAATATAACAG 58.602 37.500 0.00 0.00 34.76 3.16
2799 5374 5.048364 TGCTCCGCAAAAACAATATAACAGT 60.048 36.000 0.00 0.00 34.76 3.55
2800 5375 5.286082 GCTCCGCAAAAACAATATAACAGTG 59.714 40.000 0.00 0.00 0.00 3.66
2801 5376 5.704888 TCCGCAAAAACAATATAACAGTGG 58.295 37.500 0.00 0.00 0.00 4.00
2802 5377 4.326009 CCGCAAAAACAATATAACAGTGGC 59.674 41.667 0.00 0.00 0.00 5.01
2803 5378 5.160641 CGCAAAAACAATATAACAGTGGCT 58.839 37.500 0.00 0.00 0.00 4.75
2804 5379 5.286082 CGCAAAAACAATATAACAGTGGCTC 59.714 40.000 0.00 0.00 0.00 4.70
2805 5380 6.155827 GCAAAAACAATATAACAGTGGCTCA 58.844 36.000 0.00 0.00 0.00 4.26
2806 5381 6.644592 GCAAAAACAATATAACAGTGGCTCAA 59.355 34.615 0.00 0.00 0.00 3.02
2807 5382 7.331687 GCAAAAACAATATAACAGTGGCTCAAT 59.668 33.333 0.00 0.00 0.00 2.57
2808 5383 8.649841 CAAAAACAATATAACAGTGGCTCAATG 58.350 33.333 0.00 1.82 35.46 2.82
2809 5384 5.505173 ACAATATAACAGTGGCTCAATGC 57.495 39.130 0.00 0.00 41.94 3.56
2810 5385 4.035558 ACAATATAACAGTGGCTCAATGCG 59.964 41.667 0.00 0.00 44.05 4.73
2811 5386 2.113860 ATAACAGTGGCTCAATGCGT 57.886 45.000 0.00 0.00 44.05 5.24
2812 5387 1.155889 TAACAGTGGCTCAATGCGTG 58.844 50.000 0.00 0.00 44.05 5.34
2813 5388 0.534877 AACAGTGGCTCAATGCGTGA 60.535 50.000 0.00 0.00 44.05 4.35
2814 5389 1.230635 ACAGTGGCTCAATGCGTGAC 61.231 55.000 0.00 0.00 44.05 3.67
2815 5390 2.029288 AGTGGCTCAATGCGTGACG 61.029 57.895 0.00 0.00 44.05 4.35
2816 5391 2.030412 TGGCTCAATGCGTGACGT 59.970 55.556 6.91 0.00 44.05 4.34
2817 5392 1.011968 GTGGCTCAATGCGTGACGTA 61.012 55.000 6.91 1.26 44.05 3.57
2818 5393 0.319986 TGGCTCAATGCGTGACGTAA 60.320 50.000 6.91 0.00 44.05 3.18
2819 5394 0.370273 GGCTCAATGCGTGACGTAAG 59.630 55.000 6.91 0.00 44.05 2.34
2820 5395 0.247301 GCTCAATGCGTGACGTAAGC 60.247 55.000 6.91 4.55 45.62 3.09
2821 5396 1.350193 CTCAATGCGTGACGTAAGCT 58.650 50.000 6.91 0.00 45.62 3.74
2822 5397 1.726791 CTCAATGCGTGACGTAAGCTT 59.273 47.619 6.91 3.48 45.62 3.74
2823 5398 1.459209 TCAATGCGTGACGTAAGCTTG 59.541 47.619 9.86 4.17 45.62 4.01
2824 5399 0.165944 AATGCGTGACGTAAGCTTGC 59.834 50.000 9.86 6.89 45.62 4.01
2825 5400 1.955529 ATGCGTGACGTAAGCTTGCG 61.956 55.000 31.30 31.30 45.62 4.85
2826 5401 2.369629 GCGTGACGTAAGCTTGCGA 61.370 57.895 37.75 18.02 45.62 5.10
2827 5402 1.683790 GCGTGACGTAAGCTTGCGAT 61.684 55.000 37.75 23.73 45.62 4.58
2828 5403 0.023732 CGTGACGTAAGCTTGCGATG 59.976 55.000 37.75 20.73 45.62 3.84
2829 5404 1.346365 GTGACGTAAGCTTGCGATGA 58.654 50.000 37.75 20.19 45.62 2.92
2830 5405 1.724623 GTGACGTAAGCTTGCGATGAA 59.275 47.619 37.75 19.29 45.62 2.57
2831 5406 1.992667 TGACGTAAGCTTGCGATGAAG 59.007 47.619 37.75 12.91 45.62 3.02
2832 5407 1.993370 GACGTAAGCTTGCGATGAAGT 59.007 47.619 37.75 18.30 45.62 3.01
2833 5408 3.176708 GACGTAAGCTTGCGATGAAGTA 58.823 45.455 37.75 0.00 45.62 2.24
2834 5409 3.179830 ACGTAAGCTTGCGATGAAGTAG 58.820 45.455 37.75 10.83 45.62 2.57
2835 5410 3.179830 CGTAAGCTTGCGATGAAGTAGT 58.820 45.455 29.84 0.00 38.60 2.73
2836 5411 3.240861 CGTAAGCTTGCGATGAAGTAGTC 59.759 47.826 29.84 0.00 38.60 2.59
2837 5412 1.914634 AGCTTGCGATGAAGTAGTCG 58.085 50.000 0.00 0.00 40.62 4.18
2838 5413 1.472878 AGCTTGCGATGAAGTAGTCGA 59.527 47.619 0.00 0.00 40.11 4.20
2839 5414 1.584308 GCTTGCGATGAAGTAGTCGAC 59.416 52.381 7.70 7.70 40.11 4.20
2840 5415 2.863739 CTTGCGATGAAGTAGTCGACA 58.136 47.619 19.50 0.48 40.11 4.35
2841 5416 3.242518 CTTGCGATGAAGTAGTCGACAA 58.757 45.455 19.50 0.00 40.11 3.18
2842 5417 3.291809 TGCGATGAAGTAGTCGACAAA 57.708 42.857 19.50 1.91 40.11 2.83
2843 5418 3.242518 TGCGATGAAGTAGTCGACAAAG 58.757 45.455 19.50 0.00 40.11 2.77
2844 5419 3.243336 GCGATGAAGTAGTCGACAAAGT 58.757 45.455 19.50 5.35 40.11 2.66
2845 5420 4.083164 TGCGATGAAGTAGTCGACAAAGTA 60.083 41.667 19.50 0.00 40.11 2.24
2846 5421 4.496183 GCGATGAAGTAGTCGACAAAGTAG 59.504 45.833 19.50 1.69 40.11 2.57
2847 5422 4.496183 CGATGAAGTAGTCGACAAAGTAGC 59.504 45.833 19.50 1.28 40.11 3.58
2848 5423 5.642686 GATGAAGTAGTCGACAAAGTAGCT 58.357 41.667 19.50 0.00 0.00 3.32
2849 5424 6.456584 CGATGAAGTAGTCGACAAAGTAGCTA 60.457 42.308 19.50 0.00 40.11 3.32
2850 5425 6.564709 TGAAGTAGTCGACAAAGTAGCTAA 57.435 37.500 19.50 0.00 0.00 3.09
2851 5426 6.973843 TGAAGTAGTCGACAAAGTAGCTAAA 58.026 36.000 19.50 0.00 0.00 1.85
2852 5427 7.428020 TGAAGTAGTCGACAAAGTAGCTAAAA 58.572 34.615 19.50 0.00 0.00 1.52
2853 5428 8.086522 TGAAGTAGTCGACAAAGTAGCTAAAAT 58.913 33.333 19.50 0.00 0.00 1.82
2854 5429 8.828688 AAGTAGTCGACAAAGTAGCTAAAATT 57.171 30.769 19.50 0.00 0.00 1.82
2855 5430 8.463456 AGTAGTCGACAAAGTAGCTAAAATTC 57.537 34.615 19.50 0.00 0.00 2.17
2856 5431 8.086522 AGTAGTCGACAAAGTAGCTAAAATTCA 58.913 33.333 19.50 0.00 0.00 2.57
2857 5432 7.907214 AGTCGACAAAGTAGCTAAAATTCAT 57.093 32.000 19.50 0.00 0.00 2.57
2858 5433 7.965045 AGTCGACAAAGTAGCTAAAATTCATC 58.035 34.615 19.50 0.00 0.00 2.92
2859 5434 7.064728 AGTCGACAAAGTAGCTAAAATTCATCC 59.935 37.037 19.50 0.00 0.00 3.51
2860 5435 7.064728 GTCGACAAAGTAGCTAAAATTCATCCT 59.935 37.037 11.55 0.00 0.00 3.24
2861 5436 7.277981 TCGACAAAGTAGCTAAAATTCATCCTC 59.722 37.037 0.00 0.00 0.00 3.71
2862 5437 7.466050 CGACAAAGTAGCTAAAATTCATCCTCC 60.466 40.741 0.00 0.00 0.00 4.30
2863 5438 7.175104 ACAAAGTAGCTAAAATTCATCCTCCA 58.825 34.615 0.00 0.00 0.00 3.86
2864 5439 7.121315 ACAAAGTAGCTAAAATTCATCCTCCAC 59.879 37.037 0.00 0.00 0.00 4.02
2865 5440 5.360591 AGTAGCTAAAATTCATCCTCCACG 58.639 41.667 0.00 0.00 0.00 4.94
2866 5441 3.545703 AGCTAAAATTCATCCTCCACGG 58.454 45.455 0.00 0.00 0.00 4.94
2867 5442 2.618709 GCTAAAATTCATCCTCCACGGG 59.381 50.000 0.00 0.00 0.00 5.28
2868 5443 2.899303 AAAATTCATCCTCCACGGGT 57.101 45.000 0.00 0.00 0.00 5.28
2869 5444 2.420058 AAATTCATCCTCCACGGGTC 57.580 50.000 0.00 0.00 0.00 4.46
2870 5445 1.285280 AATTCATCCTCCACGGGTCA 58.715 50.000 0.00 0.00 0.00 4.02
2871 5446 1.511613 ATTCATCCTCCACGGGTCAT 58.488 50.000 0.00 0.00 0.00 3.06
2872 5447 0.541392 TTCATCCTCCACGGGTCATG 59.459 55.000 0.00 0.00 0.00 3.07
2873 5448 1.146930 CATCCTCCACGGGTCATGG 59.853 63.158 0.00 0.00 38.71 3.66
2874 5449 2.746375 ATCCTCCACGGGTCATGGC 61.746 63.158 0.00 0.00 37.13 4.40
2875 5450 3.402681 CCTCCACGGGTCATGGCT 61.403 66.667 0.00 0.00 37.13 4.75
2876 5451 2.671070 CTCCACGGGTCATGGCTT 59.329 61.111 0.00 0.00 37.13 4.35
2877 5452 1.746615 CTCCACGGGTCATGGCTTG 60.747 63.158 0.00 0.00 37.13 4.01
2878 5453 2.751436 CCACGGGTCATGGCTTGG 60.751 66.667 0.00 0.00 0.00 3.61
2879 5454 2.751436 CACGGGTCATGGCTTGGG 60.751 66.667 0.00 0.00 0.00 4.12
2880 5455 4.740822 ACGGGTCATGGCTTGGGC 62.741 66.667 0.00 0.00 37.82 5.36
2884 5459 3.064324 GTCATGGCTTGGGCGCTT 61.064 61.111 7.64 0.00 39.81 4.68
2885 5460 2.751436 TCATGGCTTGGGCGCTTC 60.751 61.111 7.64 0.02 39.81 3.86
2886 5461 2.753043 CATGGCTTGGGCGCTTCT 60.753 61.111 7.64 0.00 39.81 2.85
2887 5462 2.036256 ATGGCTTGGGCGCTTCTT 59.964 55.556 7.64 0.00 39.81 2.52
2888 5463 2.048603 ATGGCTTGGGCGCTTCTTC 61.049 57.895 7.64 0.00 39.81 2.87
2889 5464 2.672996 GGCTTGGGCGCTTCTTCA 60.673 61.111 7.64 0.00 39.81 3.02
2890 5465 2.268076 GGCTTGGGCGCTTCTTCAA 61.268 57.895 7.64 4.09 39.81 2.69
2891 5466 1.659794 GCTTGGGCGCTTCTTCAAA 59.340 52.632 7.64 0.00 0.00 2.69
2892 5467 0.244721 GCTTGGGCGCTTCTTCAAAT 59.755 50.000 7.64 0.00 0.00 2.32
2893 5468 1.986698 CTTGGGCGCTTCTTCAAATG 58.013 50.000 7.64 0.00 0.00 2.32
2894 5469 1.541147 CTTGGGCGCTTCTTCAAATGA 59.459 47.619 7.64 0.00 0.00 2.57
2895 5470 1.614996 TGGGCGCTTCTTCAAATGAA 58.385 45.000 7.64 0.00 0.00 2.57
2896 5471 2.170166 TGGGCGCTTCTTCAAATGAAT 58.830 42.857 7.64 0.00 33.01 2.57
2897 5472 2.094597 TGGGCGCTTCTTCAAATGAATG 60.095 45.455 7.64 0.00 33.01 2.67
2898 5473 2.533266 GGCGCTTCTTCAAATGAATGG 58.467 47.619 7.64 0.00 33.01 3.16
2899 5474 2.533266 GCGCTTCTTCAAATGAATGGG 58.467 47.619 0.00 1.22 33.01 4.00
2900 5475 2.094545 GCGCTTCTTCAAATGAATGGGT 60.095 45.455 0.00 0.00 33.01 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 2.284625 TGGCAGAGGGGACACGAT 60.285 61.111 0.00 0.00 0.00 3.73
173 174 1.069427 CCGTCCGTACCAAACCACA 59.931 57.895 0.00 0.00 0.00 4.17
363 372 3.179888 TTGCGCTCGGTTTGGGGTA 62.180 57.895 9.73 0.00 0.00 3.69
491 500 0.968901 TCGCGTCACCCTATCCTGTT 60.969 55.000 5.77 0.00 0.00 3.16
505 514 3.706373 AGGCCAACTCCATCGCGT 61.706 61.111 5.01 0.00 0.00 6.01
510 519 1.229951 TCCCTCAGGCCAACTCCAT 60.230 57.895 5.01 0.00 0.00 3.41
533 542 1.538950 GACCCTTTCTTTCTGCTGCAG 59.461 52.381 23.31 23.31 0.00 4.41
538 547 2.568623 TGGAGACCCTTTCTTTCTGC 57.431 50.000 0.00 0.00 33.22 4.26
541 550 5.826208 TGTACTTTTGGAGACCCTTTCTTTC 59.174 40.000 0.00 0.00 33.22 2.62
546 555 3.889538 GCTTGTACTTTTGGAGACCCTTT 59.110 43.478 0.00 0.00 0.00 3.11
631 640 3.883744 CTCACACACGGACAGGGCC 62.884 68.421 0.00 0.00 0.00 5.80
635 644 1.270305 ACCAATCTCACACACGGACAG 60.270 52.381 0.00 0.00 0.00 3.51
654 663 4.990543 TCGTTTCATGTCTGTCATCAAC 57.009 40.909 0.00 0.00 34.09 3.18
689 698 1.211457 ACATCCATCTCTCCCTTGCAC 59.789 52.381 0.00 0.00 0.00 4.57
691 700 1.487976 TGACATCCATCTCTCCCTTGC 59.512 52.381 0.00 0.00 0.00 4.01
709 718 0.890542 GGCAATGGCAGTGACAGTGA 60.891 55.000 29.73 0.00 39.15 3.41
713 722 3.054679 AATGGCAATGGCAGTGACA 57.945 47.368 27.05 27.05 42.43 3.58
717 726 1.914263 TGGCAATGGCAATGGCAGT 60.914 52.632 25.79 10.19 46.85 4.40
718 727 2.982960 TGGCAATGGCAATGGCAG 59.017 55.556 25.79 3.56 46.85 4.85
720 729 1.720694 GCAATGGCAATGGCAATGGC 61.721 55.000 23.26 21.05 43.05 4.40
721 730 1.098712 GGCAATGGCAATGGCAATGG 61.099 55.000 23.26 12.79 42.43 3.16
754 763 2.292323 TGTACTTTCTCTCCCTCCCTCC 60.292 54.545 0.00 0.00 0.00 4.30
762 771 5.768164 AGCTAGCTAGATGTACTTTCTCTCC 59.232 44.000 25.15 0.49 0.00 3.71
764 773 6.040391 CCAAGCTAGCTAGATGTACTTTCTCT 59.960 42.308 25.15 4.21 0.00 3.10
769 778 4.956700 TCACCAAGCTAGCTAGATGTACTT 59.043 41.667 25.15 13.96 0.00 2.24
942 954 0.833287 TTCCTGCCTAAGCTAGCCAG 59.167 55.000 12.13 10.89 40.80 4.85
943 955 0.541863 GTTCCTGCCTAAGCTAGCCA 59.458 55.000 12.13 0.22 40.80 4.75
944 956 0.833949 AGTTCCTGCCTAAGCTAGCC 59.166 55.000 12.13 0.00 40.80 3.93
945 957 1.537135 CGAGTTCCTGCCTAAGCTAGC 60.537 57.143 6.62 6.62 40.80 3.42
980 1006 4.268359 CATTTTCTCCCTCTTCTTCCCTG 58.732 47.826 0.00 0.00 0.00 4.45
1011 1037 2.034687 CCCTTGTCACAGCAGGGG 59.965 66.667 6.67 0.33 46.97 4.79
1154 1180 5.123502 GTGCAGAAATGCAGATGGATATAGG 59.876 44.000 2.62 0.00 46.32 2.57
1222 1255 1.078848 CTTCCCGCACCTCTTCAGG 60.079 63.158 0.00 0.00 46.87 3.86
1303 1336 0.031616 AGATCACCCTGTCCTCCTCC 60.032 60.000 0.00 0.00 0.00 4.30
1468 1501 1.750399 GTACTGCTGGCCATGGGTG 60.750 63.158 15.13 0.00 0.00 4.61
1469 1502 2.202236 CTGTACTGCTGGCCATGGGT 62.202 60.000 15.13 7.91 0.00 4.51
1470 1503 1.452651 CTGTACTGCTGGCCATGGG 60.453 63.158 15.13 1.08 0.00 4.00
1507 1540 0.170339 GGTGCTCAACGGTAAATGGC 59.830 55.000 0.00 0.00 0.00 4.40
1513 1546 1.070105 GTGGTGGTGCTCAACGGTA 59.930 57.895 0.00 0.00 35.35 4.02
1517 1550 1.453015 TGTGGTGGTGGTGCTCAAC 60.453 57.895 0.00 0.00 0.00 3.18
1523 1556 0.320771 GAGCTAGTGTGGTGGTGGTG 60.321 60.000 0.00 0.00 0.00 4.17
1524 1557 0.471971 AGAGCTAGTGTGGTGGTGGT 60.472 55.000 0.00 0.00 0.00 4.16
1525 1558 1.204941 GTAGAGCTAGTGTGGTGGTGG 59.795 57.143 0.00 0.00 0.00 4.61
1546 1588 0.033781 GGCCTAGAGATGCAGCAGAG 59.966 60.000 4.07 0.00 0.00 3.35
1684 1735 3.714001 CTCTCCTGCAGGCCAGCA 61.714 66.667 28.91 22.70 43.35 4.41
1686 1737 2.872931 GAAGCTCTCCTGCAGGCCAG 62.873 65.000 28.91 24.28 41.41 4.85
1759 1810 3.432588 GCTGCTGCTGCTGGTGAG 61.433 66.667 22.10 9.52 40.48 3.51
1829 1883 1.135344 GTCGCCGTAGAAGAAGAAGCT 60.135 52.381 0.00 0.00 0.00 3.74
1977 2031 1.497161 ACTCCTATATATGGGGCGGC 58.503 55.000 14.63 0.00 0.00 6.53
1991 2046 4.829492 GCCATGGCTTTAATTCATACTCCT 59.171 41.667 29.98 0.00 38.26 3.69
1992 2047 4.021981 GGCCATGGCTTTAATTCATACTCC 60.022 45.833 34.70 9.62 41.60 3.85
1995 2050 3.568007 TCGGCCATGGCTTTAATTCATAC 59.432 43.478 34.70 13.40 41.60 2.39
2093 2148 4.458989 CAGCAACACCACCACATAAACTAT 59.541 41.667 0.00 0.00 0.00 2.12
2213 4139 3.394719 TGCATGTAACAGCTACAAACGA 58.605 40.909 0.00 0.00 43.75 3.85
2312 4869 3.952967 TGTACGTACATGTGGTGCCTATA 59.047 43.478 24.10 0.00 0.00 1.31
2313 4870 2.761767 TGTACGTACATGTGGTGCCTAT 59.238 45.455 24.10 0.00 0.00 2.57
2369 4926 6.970484 ACTCCATCAATTTACACTCAACAAC 58.030 36.000 0.00 0.00 0.00 3.32
2436 4993 6.706295 AGAGGAGATGTTTGAGGAGTTAAAG 58.294 40.000 0.00 0.00 0.00 1.85
2522 5082 2.355818 GGTTCCATGTGGGGTCTAGTTC 60.356 54.545 0.00 0.00 37.22 3.01
2533 5093 1.065854 GGGAGACAGAGGTTCCATGTG 60.066 57.143 4.82 0.00 32.50 3.21
2539 5099 2.640332 AGGAAAAGGGAGACAGAGGTTC 59.360 50.000 0.00 0.00 0.00 3.62
2547 5119 5.172687 AGAAGAATGAGGAAAAGGGAGAC 57.827 43.478 0.00 0.00 0.00 3.36
2559 5131 7.172361 ACGGAAGAAAGAAGAAAGAAGAATGAG 59.828 37.037 0.00 0.00 0.00 2.90
2569 5141 4.033587 CACGTGAACGGAAGAAAGAAGAAA 59.966 41.667 10.90 0.00 44.95 2.52
2614 5189 3.666374 GCTAGCGCATGCAAATCATCTAC 60.666 47.826 19.57 0.00 46.23 2.59
2625 5200 1.667467 GGAGTACTAGCTAGCGCATGC 60.667 57.143 20.91 13.80 43.24 4.06
2637 5212 2.905415 TTGGAACGGAGGGAGTACTA 57.095 50.000 0.00 0.00 0.00 1.82
2642 5217 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2643 5218 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2644 5219 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2645 5220 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2646 5221 3.846360 AGACGAGTAATTTGGAACGGAG 58.154 45.455 0.00 0.00 0.00 4.63
2647 5222 3.256383 TGAGACGAGTAATTTGGAACGGA 59.744 43.478 0.00 0.00 0.00 4.69
2648 5223 3.581755 TGAGACGAGTAATTTGGAACGG 58.418 45.455 0.00 0.00 0.00 4.44
2649 5224 4.482386 TCTGAGACGAGTAATTTGGAACG 58.518 43.478 0.00 0.00 0.00 3.95
2650 5225 6.780706 TTTCTGAGACGAGTAATTTGGAAC 57.219 37.500 0.00 0.00 0.00 3.62
2651 5226 9.496873 TTTATTTCTGAGACGAGTAATTTGGAA 57.503 29.630 0.00 0.00 0.00 3.53
2652 5227 9.496873 TTTTATTTCTGAGACGAGTAATTTGGA 57.503 29.630 0.00 0.00 0.00 3.53
2660 5235 9.877178 ACATCTATTTTTATTTCTGAGACGAGT 57.123 29.630 0.00 0.00 0.00 4.18
2700 5275 9.278978 CGCAGGTATAGATGTATCTAGATGTAT 57.721 37.037 15.79 9.11 42.20 2.29
2701 5276 8.483758 TCGCAGGTATAGATGTATCTAGATGTA 58.516 37.037 15.79 4.44 42.20 2.29
2702 5277 7.339482 TCGCAGGTATAGATGTATCTAGATGT 58.661 38.462 15.79 1.25 42.20 3.06
2703 5278 7.793927 TCGCAGGTATAGATGTATCTAGATG 57.206 40.000 15.79 0.00 42.20 2.90
2705 5280 9.549078 CTTATCGCAGGTATAGATGTATCTAGA 57.451 37.037 7.57 0.00 42.20 2.43
2706 5281 9.332502 ACTTATCGCAGGTATAGATGTATCTAG 57.667 37.037 7.57 0.00 42.20 2.43
2708 5283 9.682465 TTACTTATCGCAGGTATAGATGTATCT 57.318 33.333 0.00 0.00 40.86 1.98
2711 5286 9.293404 ACTTTACTTATCGCAGGTATAGATGTA 57.707 33.333 0.00 0.00 0.00 2.29
2712 5287 8.179509 ACTTTACTTATCGCAGGTATAGATGT 57.820 34.615 0.00 0.00 0.00 3.06
2718 5293 9.052759 CCAAATTACTTTACTTATCGCAGGTAT 57.947 33.333 0.00 0.00 0.00 2.73
2719 5294 8.259411 TCCAAATTACTTTACTTATCGCAGGTA 58.741 33.333 0.00 0.00 0.00 3.08
2720 5295 7.107542 TCCAAATTACTTTACTTATCGCAGGT 58.892 34.615 0.00 0.00 0.00 4.00
2721 5296 7.548196 TCCAAATTACTTTACTTATCGCAGG 57.452 36.000 0.00 0.00 0.00 4.85
2722 5297 7.634817 CGTTCCAAATTACTTTACTTATCGCAG 59.365 37.037 0.00 0.00 0.00 5.18
2723 5298 7.413219 CCGTTCCAAATTACTTTACTTATCGCA 60.413 37.037 0.00 0.00 0.00 5.10
2724 5299 6.903479 CCGTTCCAAATTACTTTACTTATCGC 59.097 38.462 0.00 0.00 0.00 4.58
2725 5300 8.188531 TCCGTTCCAAATTACTTTACTTATCG 57.811 34.615 0.00 0.00 0.00 2.92
2726 5301 8.610035 CCTCCGTTCCAAATTACTTTACTTATC 58.390 37.037 0.00 0.00 0.00 1.75
2727 5302 7.555195 CCCTCCGTTCCAAATTACTTTACTTAT 59.445 37.037 0.00 0.00 0.00 1.73
2728 5303 6.880529 CCCTCCGTTCCAAATTACTTTACTTA 59.119 38.462 0.00 0.00 0.00 2.24
2729 5304 5.708697 CCCTCCGTTCCAAATTACTTTACTT 59.291 40.000 0.00 0.00 0.00 2.24
2730 5305 5.013391 TCCCTCCGTTCCAAATTACTTTACT 59.987 40.000 0.00 0.00 0.00 2.24
2731 5306 5.247862 TCCCTCCGTTCCAAATTACTTTAC 58.752 41.667 0.00 0.00 0.00 2.01
2732 5307 5.013391 ACTCCCTCCGTTCCAAATTACTTTA 59.987 40.000 0.00 0.00 0.00 1.85
2733 5308 4.202535 ACTCCCTCCGTTCCAAATTACTTT 60.203 41.667 0.00 0.00 0.00 2.66
2734 5309 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
2735 5310 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2736 5311 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2737 5312 3.198417 GGTACTCCCTCCGTTCCAAATTA 59.802 47.826 0.00 0.00 0.00 1.40
2738 5313 2.026542 GGTACTCCCTCCGTTCCAAATT 60.027 50.000 0.00 0.00 0.00 1.82
2739 5314 1.558294 GGTACTCCCTCCGTTCCAAAT 59.442 52.381 0.00 0.00 0.00 2.32
2740 5315 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
2741 5316 0.115745 AGGTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 40.71 3.53
2742 5317 1.002069 TAGGTACTCCCTCCGTTCCA 58.998 55.000 0.00 0.00 44.81 3.53
2743 5318 1.689984 CTAGGTACTCCCTCCGTTCC 58.310 60.000 0.00 0.00 44.81 3.62
2744 5319 1.689984 CCTAGGTACTCCCTCCGTTC 58.310 60.000 0.00 0.00 44.81 3.95
2745 5320 0.261109 CCCTAGGTACTCCCTCCGTT 59.739 60.000 8.29 0.00 44.81 4.44
2746 5321 0.923233 ACCCTAGGTACTCCCTCCGT 60.923 60.000 8.29 0.00 44.81 4.69
2747 5322 1.143813 TACCCTAGGTACTCCCTCCG 58.856 60.000 8.29 0.00 44.81 4.63
2748 5323 6.465607 CGATATATACCCTAGGTACTCCCTCC 60.466 50.000 8.29 0.00 44.81 4.30
2749 5324 6.328672 TCGATATATACCCTAGGTACTCCCTC 59.671 46.154 8.29 0.00 44.81 4.30
2751 5326 6.506538 TCGATATATACCCTAGGTACTCCC 57.493 45.833 8.29 0.00 41.31 4.30
2752 5327 6.430616 GCATCGATATATACCCTAGGTACTCC 59.569 46.154 8.29 0.00 41.31 3.85
2753 5328 7.225725 AGCATCGATATATACCCTAGGTACTC 58.774 42.308 8.29 0.00 41.31 2.59
2754 5329 7.151694 AGCATCGATATATACCCTAGGTACT 57.848 40.000 8.29 0.00 41.31 2.73
2755 5330 6.430616 GGAGCATCGATATATACCCTAGGTAC 59.569 46.154 8.29 0.00 37.13 3.34
2756 5331 6.540995 GGAGCATCGATATATACCCTAGGTA 58.459 44.000 8.29 0.70 38.25 3.08
2757 5332 5.386924 GGAGCATCGATATATACCCTAGGT 58.613 45.833 8.29 0.00 36.14 3.08
2758 5333 4.456222 CGGAGCATCGATATATACCCTAGG 59.544 50.000 0.06 0.06 34.37 3.02
2759 5334 5.614923 CGGAGCATCGATATATACCCTAG 57.385 47.826 0.00 0.00 34.37 3.02
2777 5352 5.799936 CCACTGTTATATTGTTTTTGCGGAG 59.200 40.000 0.00 0.00 0.00 4.63
2778 5353 5.704888 CCACTGTTATATTGTTTTTGCGGA 58.295 37.500 0.00 0.00 0.00 5.54
2779 5354 4.326009 GCCACTGTTATATTGTTTTTGCGG 59.674 41.667 0.00 0.00 0.00 5.69
2780 5355 5.160641 AGCCACTGTTATATTGTTTTTGCG 58.839 37.500 0.00 0.00 0.00 4.85
2781 5356 6.155827 TGAGCCACTGTTATATTGTTTTTGC 58.844 36.000 0.00 0.00 0.00 3.68
2782 5357 8.649841 CATTGAGCCACTGTTATATTGTTTTTG 58.350 33.333 0.00 0.00 0.00 2.44
2783 5358 7.331687 GCATTGAGCCACTGTTATATTGTTTTT 59.668 33.333 0.00 0.00 37.23 1.94
2784 5359 6.813152 GCATTGAGCCACTGTTATATTGTTTT 59.187 34.615 0.00 0.00 37.23 2.43
2785 5360 6.332630 GCATTGAGCCACTGTTATATTGTTT 58.667 36.000 0.00 0.00 37.23 2.83
2786 5361 5.449041 CGCATTGAGCCACTGTTATATTGTT 60.449 40.000 0.00 0.00 41.38 2.83
2787 5362 4.035558 CGCATTGAGCCACTGTTATATTGT 59.964 41.667 0.00 0.00 41.38 2.71
2788 5363 4.035558 ACGCATTGAGCCACTGTTATATTG 59.964 41.667 0.00 0.00 41.38 1.90
2789 5364 4.035558 CACGCATTGAGCCACTGTTATATT 59.964 41.667 0.00 0.00 41.38 1.28
2790 5365 3.561310 CACGCATTGAGCCACTGTTATAT 59.439 43.478 0.00 0.00 41.38 0.86
2791 5366 2.935849 CACGCATTGAGCCACTGTTATA 59.064 45.455 0.00 0.00 41.38 0.98
2792 5367 1.739466 CACGCATTGAGCCACTGTTAT 59.261 47.619 0.00 0.00 41.38 1.89
2793 5368 1.155889 CACGCATTGAGCCACTGTTA 58.844 50.000 0.00 0.00 41.38 2.41
2794 5369 0.534877 TCACGCATTGAGCCACTGTT 60.535 50.000 0.00 0.00 41.38 3.16
2795 5370 1.071299 TCACGCATTGAGCCACTGT 59.929 52.632 0.00 0.00 41.38 3.55
2796 5371 1.499056 GTCACGCATTGAGCCACTG 59.501 57.895 0.00 0.00 41.38 3.66
2797 5372 2.029288 CGTCACGCATTGAGCCACT 61.029 57.895 0.00 0.00 41.38 4.00
2798 5373 1.011968 TACGTCACGCATTGAGCCAC 61.012 55.000 0.00 0.00 41.38 5.01
2799 5374 0.319986 TTACGTCACGCATTGAGCCA 60.320 50.000 0.00 0.00 41.38 4.75
2800 5375 0.370273 CTTACGTCACGCATTGAGCC 59.630 55.000 0.00 0.00 41.38 4.70
2801 5376 0.247301 GCTTACGTCACGCATTGAGC 60.247 55.000 0.00 0.00 33.71 4.26
2802 5377 1.350193 AGCTTACGTCACGCATTGAG 58.650 50.000 0.00 0.00 33.71 3.02
2803 5378 1.459209 CAAGCTTACGTCACGCATTGA 59.541 47.619 0.00 0.00 0.00 2.57
2804 5379 1.869503 CAAGCTTACGTCACGCATTG 58.130 50.000 0.00 0.00 0.00 2.82
2805 5380 0.165944 GCAAGCTTACGTCACGCATT 59.834 50.000 0.00 0.00 0.00 3.56
2806 5381 1.787847 GCAAGCTTACGTCACGCAT 59.212 52.632 0.00 0.00 0.00 4.73
2807 5382 2.653967 CGCAAGCTTACGTCACGCA 61.654 57.895 11.01 0.00 0.00 5.24
2808 5383 1.683790 ATCGCAAGCTTACGTCACGC 61.684 55.000 18.16 5.83 37.18 5.34
2809 5384 0.023732 CATCGCAAGCTTACGTCACG 59.976 55.000 18.16 0.00 37.18 4.35
2810 5385 1.346365 TCATCGCAAGCTTACGTCAC 58.654 50.000 18.16 0.00 37.18 3.67
2811 5386 1.992667 CTTCATCGCAAGCTTACGTCA 59.007 47.619 18.16 0.87 37.18 4.35
2812 5387 1.993370 ACTTCATCGCAAGCTTACGTC 59.007 47.619 18.16 0.00 37.18 4.34
2813 5388 2.080286 ACTTCATCGCAAGCTTACGT 57.920 45.000 18.16 3.91 37.18 3.57
2814 5389 3.179830 ACTACTTCATCGCAAGCTTACG 58.820 45.455 13.00 13.00 37.18 3.18
2815 5390 3.240861 CGACTACTTCATCGCAAGCTTAC 59.759 47.826 0.00 0.00 37.18 2.34
2816 5391 3.128068 TCGACTACTTCATCGCAAGCTTA 59.872 43.478 0.00 0.00 38.24 3.09
2817 5392 2.094700 TCGACTACTTCATCGCAAGCTT 60.095 45.455 0.00 0.00 38.24 3.74
2818 5393 1.472878 TCGACTACTTCATCGCAAGCT 59.527 47.619 0.00 0.00 38.24 3.74
2819 5394 1.584308 GTCGACTACTTCATCGCAAGC 59.416 52.381 8.70 0.00 38.24 4.01
2820 5395 2.863739 TGTCGACTACTTCATCGCAAG 58.136 47.619 17.92 0.00 38.24 4.01
2821 5396 3.291809 TTGTCGACTACTTCATCGCAA 57.708 42.857 17.92 0.00 38.24 4.85
2822 5397 3.242518 CTTTGTCGACTACTTCATCGCA 58.757 45.455 17.92 0.00 38.24 5.10
2823 5398 3.243336 ACTTTGTCGACTACTTCATCGC 58.757 45.455 17.92 0.00 38.24 4.58
2824 5399 4.496183 GCTACTTTGTCGACTACTTCATCG 59.504 45.833 17.92 0.00 39.72 3.84
2825 5400 5.642686 AGCTACTTTGTCGACTACTTCATC 58.357 41.667 17.92 0.27 0.00 2.92
2826 5401 5.646577 AGCTACTTTGTCGACTACTTCAT 57.353 39.130 17.92 0.00 0.00 2.57
2827 5402 6.564709 TTAGCTACTTTGTCGACTACTTCA 57.435 37.500 17.92 0.00 0.00 3.02
2828 5403 7.864307 TTTTAGCTACTTTGTCGACTACTTC 57.136 36.000 17.92 0.29 0.00 3.01
2829 5404 8.828688 AATTTTAGCTACTTTGTCGACTACTT 57.171 30.769 17.92 0.97 0.00 2.24
2830 5405 8.086522 TGAATTTTAGCTACTTTGTCGACTACT 58.913 33.333 17.92 4.80 0.00 2.57
2831 5406 8.236084 TGAATTTTAGCTACTTTGTCGACTAC 57.764 34.615 17.92 0.00 0.00 2.73
2832 5407 8.997621 ATGAATTTTAGCTACTTTGTCGACTA 57.002 30.769 17.92 6.32 0.00 2.59
2833 5408 7.064728 GGATGAATTTTAGCTACTTTGTCGACT 59.935 37.037 17.92 0.00 0.00 4.18
2834 5409 7.064728 AGGATGAATTTTAGCTACTTTGTCGAC 59.935 37.037 9.11 9.11 0.00 4.20
2835 5410 7.103641 AGGATGAATTTTAGCTACTTTGTCGA 58.896 34.615 0.00 0.00 0.00 4.20
2836 5411 7.308782 AGGATGAATTTTAGCTACTTTGTCG 57.691 36.000 0.00 0.00 0.00 4.35
2837 5412 7.336931 TGGAGGATGAATTTTAGCTACTTTGTC 59.663 37.037 0.00 0.00 0.00 3.18
2838 5413 7.121315 GTGGAGGATGAATTTTAGCTACTTTGT 59.879 37.037 0.00 0.00 0.00 2.83
2839 5414 7.475840 GTGGAGGATGAATTTTAGCTACTTTG 58.524 38.462 0.00 0.00 0.00 2.77
2840 5415 6.316390 CGTGGAGGATGAATTTTAGCTACTTT 59.684 38.462 0.00 0.00 0.00 2.66
2841 5416 5.817816 CGTGGAGGATGAATTTTAGCTACTT 59.182 40.000 0.00 0.00 0.00 2.24
2842 5417 5.360591 CGTGGAGGATGAATTTTAGCTACT 58.639 41.667 0.00 0.00 0.00 2.57
2843 5418 4.511826 CCGTGGAGGATGAATTTTAGCTAC 59.488 45.833 0.00 0.00 45.00 3.58
2844 5419 4.444306 CCCGTGGAGGATGAATTTTAGCTA 60.444 45.833 0.00 0.00 45.00 3.32
2845 5420 3.545703 CCGTGGAGGATGAATTTTAGCT 58.454 45.455 0.00 0.00 45.00 3.32
2846 5421 2.618709 CCCGTGGAGGATGAATTTTAGC 59.381 50.000 0.00 0.00 45.00 3.09
2847 5422 3.877508 GACCCGTGGAGGATGAATTTTAG 59.122 47.826 0.00 0.00 45.00 1.85
2848 5423 3.264706 TGACCCGTGGAGGATGAATTTTA 59.735 43.478 0.00 0.00 45.00 1.52
2849 5424 2.041081 TGACCCGTGGAGGATGAATTTT 59.959 45.455 0.00 0.00 45.00 1.82
2850 5425 1.633432 TGACCCGTGGAGGATGAATTT 59.367 47.619 0.00 0.00 45.00 1.82
2851 5426 1.285280 TGACCCGTGGAGGATGAATT 58.715 50.000 0.00 0.00 45.00 2.17
2852 5427 1.141657 CATGACCCGTGGAGGATGAAT 59.858 52.381 0.00 0.00 45.00 2.57
2853 5428 0.541392 CATGACCCGTGGAGGATGAA 59.459 55.000 0.00 0.00 45.00 2.57
2854 5429 1.337384 CCATGACCCGTGGAGGATGA 61.337 60.000 0.00 0.00 42.73 2.92
2855 5430 1.146930 CCATGACCCGTGGAGGATG 59.853 63.158 0.00 0.00 42.73 3.51
2856 5431 2.746375 GCCATGACCCGTGGAGGAT 61.746 63.158 9.24 0.00 42.73 3.24
2857 5432 3.399181 GCCATGACCCGTGGAGGA 61.399 66.667 9.24 0.00 42.73 3.71
2858 5433 2.971598 AAGCCATGACCCGTGGAGG 61.972 63.158 9.24 0.00 42.73 4.30
2859 5434 1.746615 CAAGCCATGACCCGTGGAG 60.747 63.158 9.24 0.00 42.73 3.86
2860 5435 2.350895 CAAGCCATGACCCGTGGA 59.649 61.111 9.24 0.00 42.73 4.02
2861 5436 2.751436 CCAAGCCATGACCCGTGG 60.751 66.667 0.00 0.97 42.95 4.94
2862 5437 2.751436 CCCAAGCCATGACCCGTG 60.751 66.667 0.00 0.00 0.00 4.94
2863 5438 4.740822 GCCCAAGCCATGACCCGT 62.741 66.667 0.00 0.00 0.00 5.28
2867 5442 3.056313 GAAGCGCCCAAGCCATGAC 62.056 63.158 2.29 0.00 38.01 3.06
2868 5443 2.751436 GAAGCGCCCAAGCCATGA 60.751 61.111 2.29 0.00 38.01 3.07
2869 5444 2.275547 GAAGAAGCGCCCAAGCCATG 62.276 60.000 2.29 0.00 38.01 3.66
2870 5445 2.036256 AAGAAGCGCCCAAGCCAT 59.964 55.556 2.29 0.00 38.01 4.40
2871 5446 2.672996 GAAGAAGCGCCCAAGCCA 60.673 61.111 2.29 0.00 38.01 4.75
2872 5447 1.805428 TTTGAAGAAGCGCCCAAGCC 61.805 55.000 2.29 0.00 38.01 4.35
2873 5448 0.244721 ATTTGAAGAAGCGCCCAAGC 59.755 50.000 2.29 0.00 37.41 4.01
2874 5449 1.541147 TCATTTGAAGAAGCGCCCAAG 59.459 47.619 2.29 0.00 0.00 3.61
2875 5450 1.614996 TCATTTGAAGAAGCGCCCAA 58.385 45.000 2.29 0.00 0.00 4.12
2876 5451 1.614996 TTCATTTGAAGAAGCGCCCA 58.385 45.000 2.29 0.00 0.00 5.36
2877 5452 2.533266 CATTCATTTGAAGAAGCGCCC 58.467 47.619 2.29 0.00 37.48 6.13
2878 5453 2.533266 CCATTCATTTGAAGAAGCGCC 58.467 47.619 2.29 0.00 37.48 6.53
2879 5454 2.094545 ACCCATTCATTTGAAGAAGCGC 60.095 45.455 0.00 0.00 37.48 5.92
2880 5455 3.855689 ACCCATTCATTTGAAGAAGCG 57.144 42.857 0.00 0.00 37.48 4.68


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

AutoCloner maintained by Alex Coulton.