Multiple sequence alignment - TraesCS7A01G261700

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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 TraesCS7A01G261700 chr7A 100.000 4421 0 0 1 4421 256216597 256212177 0.000000e+00 8165.0
1 TraesCS7A01G261700 chr7B 90.231 3685 187 87 806 4400 217623735 217627336 0.000000e+00 4650.0
2 TraesCS7A01G261700 chr7B 88.298 282 26 6 475 753 217623470 217623747 9.170000e-87 331.0
3 TraesCS7A01G261700 chr7B 89.630 135 14 0 1 135 94208825 94208691 5.880000e-39 172.0
4 TraesCS7A01G261700 chr7B 89.706 136 12 1 2 135 349492158 349492293 5.880000e-39 172.0
5 TraesCS7A01G261700 chr7B 82.105 95 12 4 167 256 346232718 346232812 4.740000e-10 76.8
6 TraesCS7A01G261700 chr7D 92.564 3066 109 51 802 3826 241880866 241883853 0.000000e+00 4289.0
7 TraesCS7A01G261700 chr7D 89.550 756 70 4 1 756 241880135 241880881 0.000000e+00 950.0
8 TraesCS7A01G261700 chr7D 81.667 540 45 32 3909 4421 241884000 241884512 2.480000e-107 399.0
9 TraesCS7A01G261700 chr7D 83.158 95 11 4 167 256 546540254 546540348 1.020000e-11 82.4
10 TraesCS7A01G261700 chr5B 81.208 298 46 6 166 462 689868965 689868677 9.560000e-57 231.0
11 TraesCS7A01G261700 chr2D 82.072 251 41 3 166 416 605473643 605473397 1.250000e-50 211.0
12 TraesCS7A01G261700 chr2A 80.451 266 45 4 169 433 736755731 736755472 3.490000e-46 196.0
13 TraesCS7A01G261700 chr1B 87.662 154 15 3 1 150 568231247 568231400 4.540000e-40 176.0
14 TraesCS7A01G261700 chr1B 87.162 148 15 3 1 144 654884098 654883951 9.840000e-37 165.0
15 TraesCS7A01G261700 chr4B 88.356 146 13 3 1 143 500322139 500322283 5.880000e-39 172.0
16 TraesCS7A01G261700 chr4B 87.586 145 16 2 1 144 88778631 88778774 2.740000e-37 167.0
17 TraesCS7A01G261700 chr4B 77.181 149 34 0 2264 2412 469034938 469034790 2.190000e-13 87.9
18 TraesCS7A01G261700 chr3A 89.630 135 14 0 1 135 589915779 589915645 5.880000e-39 172.0
19 TraesCS7A01G261700 chr2B 88.971 136 15 0 1 136 752516682 752516547 7.600000e-38 169.0
20 TraesCS7A01G261700 chr4A 80.899 178 29 3 260 433 119637899 119637723 7.710000e-28 135.0
21 TraesCS7A01G261700 chr4A 80.597 134 26 0 2264 2397 81800388 81800521 2.180000e-18 104.0
22 TraesCS7A01G261700 chr6B 82.000 150 23 4 3079 3226 471630547 471630694 1.670000e-24 124.0
23 TraesCS7A01G261700 chr6A 81.879 149 25 2 3079 3226 409413831 409413978 1.670000e-24 124.0
24 TraesCS7A01G261700 chr6A 81.169 154 29 0 166 319 602590637 602590484 1.670000e-24 124.0
25 TraesCS7A01G261700 chr6A 82.105 95 12 4 167 256 457488475 457488569 4.740000e-10 76.8
26 TraesCS7A01G261700 chr6D 80.380 158 29 2 3079 3235 305179756 305179600 7.770000e-23 119.0
27 TraesCS7A01G261700 chr4D 77.852 149 33 0 2264 2412 381888642 381888494 4.710000e-15 93.5
28 TraesCS7A01G261700 chr3B 81.633 98 13 4 167 259 567566585 567566488 4.740000e-10 76.8


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 TraesCS7A01G261700 chr7A 256212177 256216597 4420 True 8165.000000 8165 100.0000 1 4421 1 chr7A.!!$R1 4420
1 TraesCS7A01G261700 chr7B 217623470 217627336 3866 False 2490.500000 4650 89.2645 475 4400 2 chr7B.!!$F3 3925
2 TraesCS7A01G261700 chr7D 241880135 241884512 4377 False 1879.333333 4289 87.9270 1 4421 3 chr7D.!!$F2 4420

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
568 569 0.032540 CCAGGCACAGAAACAAAGCC 59.967 55.0 0.0 0.0 45.54 4.35 F
1130 1157 0.178964 TTTCTGCCCCCTTTGACCTG 60.179 55.0 0.0 0.0 0.00 4.00 F
2519 2555 0.246086 CAGTGCCACTCTCCAGTCTC 59.754 60.0 0.0 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2529 2565 0.031994 AACCGGTGAAAATGCTGTGC 59.968 50.0 8.52 0.0 0.0 4.57 R
2778 2818 0.176219 CCCATTCTGCCCGTACGTTA 59.824 55.0 15.21 0.0 0.0 3.18 R
4374 4558 0.047176 TCTCTCTCCCTCTCCCTCCT 59.953 60.0 0.00 0.0 0.0 3.69 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
29 30 3.342627 GTTGCACGGCACTGCGTA 61.343 61.111 0.00 0.00 38.71 4.42
30 31 2.589159 TTGCACGGCACTGCGTAA 60.589 55.556 0.00 0.00 38.71 3.18
31 32 2.603247 TTGCACGGCACTGCGTAAG 61.603 57.895 0.00 0.00 38.71 2.34
60 61 0.244994 CGATCCGTGATCCATCTCCC 59.755 60.000 7.91 0.00 35.83 4.30
71 72 1.837439 TCCATCTCCCGTAGCATGTTT 59.163 47.619 0.00 0.00 0.00 2.83
81 82 3.440173 CCGTAGCATGTTTCTGGATGTTT 59.560 43.478 0.00 0.00 0.00 2.83
94 95 2.291282 TGGATGTTTTGCGGGTAGGAAT 60.291 45.455 0.00 0.00 0.00 3.01
101 102 6.760291 TGTTTTGCGGGTAGGAATTTTAATT 58.240 32.000 0.00 0.00 0.00 1.40
102 103 7.217906 TGTTTTGCGGGTAGGAATTTTAATTT 58.782 30.769 0.00 0.00 0.00 1.82
120 121 2.089887 TTGCAGTCGACGCACCCTAA 62.090 55.000 26.64 14.22 39.59 2.69
121 122 2.092882 GCAGTCGACGCACCCTAAC 61.093 63.158 21.73 0.00 0.00 2.34
143 144 7.781548 AACGTAGAACCCAACATTACATATC 57.218 36.000 0.00 0.00 0.00 1.63
154 155 8.432805 CCCAACATTACATATCTTCTACCTCTT 58.567 37.037 0.00 0.00 0.00 2.85
174 175 9.924010 ACCTCTTCTACTTATGTATGTTCTAGT 57.076 33.333 0.00 0.00 0.00 2.57
206 207 0.531974 TGACCGCACCTTCACTTCAC 60.532 55.000 0.00 0.00 0.00 3.18
207 208 0.531974 GACCGCACCTTCACTTCACA 60.532 55.000 0.00 0.00 0.00 3.58
279 280 3.495453 CGGAAGGGAACAACAAGGACTTA 60.495 47.826 0.00 0.00 0.00 2.24
288 289 1.901591 ACAAGGACTTAGACGACGGA 58.098 50.000 0.00 0.00 0.00 4.69
292 293 1.226239 GACTTAGACGACGGACGCC 60.226 63.158 0.00 0.00 46.94 5.68
314 315 2.360483 GCCGTAGTCTAGGTTTAGGTCC 59.640 54.545 0.00 0.00 0.00 4.46
317 318 2.915657 AGTCTAGGTTTAGGTCCGGT 57.084 50.000 0.00 0.00 0.00 5.28
324 325 0.694771 GTTTAGGTCCGGTCCCCTTT 59.305 55.000 14.60 0.00 32.08 3.11
337 338 4.986034 CGGTCCCCTTTTGTTAATGAAAAC 59.014 41.667 0.00 0.00 0.00 2.43
339 340 6.016108 CGGTCCCCTTTTGTTAATGAAAACTA 60.016 38.462 0.00 0.00 0.00 2.24
342 343 8.803235 GTCCCCTTTTGTTAATGAAAACTATCT 58.197 33.333 0.00 0.00 0.00 1.98
364 365 0.806868 AATGCAGTGAATGTGCTCCG 59.193 50.000 0.00 0.00 41.78 4.63
365 366 0.321919 ATGCAGTGAATGTGCTCCGT 60.322 50.000 0.00 0.00 41.78 4.69
374 375 4.068599 TGAATGTGCTCCGTTTTGTATGA 58.931 39.130 0.00 0.00 0.00 2.15
382 383 6.687105 GTGCTCCGTTTTGTATGAATATCAAC 59.313 38.462 0.00 0.00 0.00 3.18
401 402 4.981674 TCAACTTGTTTCCATGATTTTCGC 59.018 37.500 0.00 0.00 0.00 4.70
404 405 4.278170 ACTTGTTTCCATGATTTTCGCTCA 59.722 37.500 0.00 0.00 0.00 4.26
408 409 4.424061 TTCCATGATTTTCGCTCAGTTG 57.576 40.909 0.00 0.00 0.00 3.16
417 418 2.031258 TCGCTCAGTTGGTTGAAACA 57.969 45.000 0.00 0.00 32.21 2.83
421 422 3.303132 CGCTCAGTTGGTTGAAACACTAC 60.303 47.826 0.00 0.00 32.21 2.73
441 442 8.368668 ACACTACTTGAAATGTATAGGGATAGC 58.631 37.037 0.00 0.00 0.00 2.97
442 443 8.367911 CACTACTTGAAATGTATAGGGATAGCA 58.632 37.037 0.00 0.00 0.00 3.49
443 444 9.105844 ACTACTTGAAATGTATAGGGATAGCAT 57.894 33.333 0.00 0.00 0.00 3.79
446 447 9.726438 ACTTGAAATGTATAGGGATAGCATAAC 57.274 33.333 0.00 0.00 0.00 1.89
462 463 4.462483 AGCATAACATTGAATGACCGGTTT 59.538 37.500 9.42 0.00 0.00 3.27
463 464 5.047377 AGCATAACATTGAATGACCGGTTTT 60.047 36.000 9.42 5.90 0.00 2.43
466 467 2.882137 ACATTGAATGACCGGTTTTCGT 59.118 40.909 9.42 6.50 37.11 3.85
471 472 5.327616 TGAATGACCGGTTTTCGTATCTA 57.672 39.130 9.42 0.00 37.11 1.98
482 483 5.860716 GGTTTTCGTATCTATATCCGTGGAC 59.139 44.000 0.00 0.00 0.00 4.02
487 488 5.585047 TCGTATCTATATCCGTGGACAGATG 59.415 44.000 14.96 4.85 0.00 2.90
489 490 6.127980 CGTATCTATATCCGTGGACAGATGTT 60.128 42.308 14.96 0.00 0.00 2.71
504 505 3.126858 CAGATGTTGTGTCCGGTTTATGG 59.873 47.826 0.00 0.00 0.00 2.74
549 550 3.447918 AGCAAGCATGTCAAATATGGC 57.552 42.857 0.00 0.00 0.00 4.40
568 569 0.032540 CCAGGCACAGAAACAAAGCC 59.967 55.000 0.00 0.00 45.54 4.35
602 603 2.491693 TGATCTTTTCGCCCAAACATCC 59.508 45.455 0.00 0.00 0.00 3.51
616 617 0.323999 ACATCCCCCTTTAAACCGGC 60.324 55.000 0.00 0.00 0.00 6.13
631 632 2.430367 GGCGAAGGGACACCAACT 59.570 61.111 0.00 0.00 40.13 3.16
771 775 4.687262 ATATATCTCCCCCGTAAGTCCA 57.313 45.455 0.00 0.00 0.00 4.02
772 776 3.562108 ATATCTCCCCCGTAAGTCCAT 57.438 47.619 0.00 0.00 0.00 3.41
773 777 4.687262 ATATCTCCCCCGTAAGTCCATA 57.313 45.455 0.00 0.00 0.00 2.74
774 778 2.852714 TCTCCCCCGTAAGTCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
775 779 3.119009 TCTCCCCCGTAAGTCCATAAA 57.881 47.619 0.00 0.00 0.00 1.40
776 780 2.767960 TCTCCCCCGTAAGTCCATAAAC 59.232 50.000 0.00 0.00 0.00 2.01
777 781 2.502538 CTCCCCCGTAAGTCCATAAACA 59.497 50.000 0.00 0.00 0.00 2.83
778 782 2.911636 TCCCCCGTAAGTCCATAAACAA 59.088 45.455 0.00 0.00 0.00 2.83
779 783 3.330110 TCCCCCGTAAGTCCATAAACAAA 59.670 43.478 0.00 0.00 0.00 2.83
780 784 4.018233 TCCCCCGTAAGTCCATAAACAAAT 60.018 41.667 0.00 0.00 0.00 2.32
781 785 5.191323 TCCCCCGTAAGTCCATAAACAAATA 59.809 40.000 0.00 0.00 0.00 1.40
782 786 6.066032 CCCCCGTAAGTCCATAAACAAATAT 58.934 40.000 0.00 0.00 0.00 1.28
783 787 7.072202 TCCCCCGTAAGTCCATAAACAAATATA 59.928 37.037 0.00 0.00 0.00 0.86
784 788 7.886446 CCCCCGTAAGTCCATAAACAAATATAT 59.114 37.037 0.00 0.00 0.00 0.86
785 789 9.947433 CCCCGTAAGTCCATAAACAAATATATA 57.053 33.333 0.00 0.00 0.00 0.86
1090 1117 2.354203 CCAAGGTTTCTCTCCTTCCTCG 60.354 54.545 0.00 0.00 42.57 4.63
1119 1146 1.073923 TGTTCTTCCTCCTTTCTGCCC 59.926 52.381 0.00 0.00 0.00 5.36
1130 1157 0.178964 TTTCTGCCCCCTTTGACCTG 60.179 55.000 0.00 0.00 0.00 4.00
1240 1267 2.610727 GGTCAAGGTACAGACACAGCTC 60.611 54.545 12.46 0.00 37.37 4.09
1321 1348 4.829064 TGCATAATTATTTCTCACGCCC 57.171 40.909 0.00 0.00 0.00 6.13
1518 1545 1.112113 TAAGGAGGAAGCTAGCGTGG 58.888 55.000 8.23 0.00 0.00 4.94
1657 1685 3.063180 GCCAAGTCATCGACAGAATTGAG 59.937 47.826 23.36 16.59 41.96 3.02
1672 1700 7.097834 ACAGAATTGAGCAGGTAAAGTACTAC 58.902 38.462 0.00 0.00 0.00 2.73
1686 1714 4.489306 AGTACTACAAAGAATCCCAGCC 57.511 45.455 0.00 0.00 0.00 4.85
1736 1764 1.303074 TGGCAAAGGCAGAGCAGAG 60.303 57.895 0.00 0.00 43.71 3.35
1748 1776 4.188702 GCAGAGTGCAGAGCAGAG 57.811 61.111 0.00 0.00 44.26 3.35
1767 1797 2.149578 AGTGTGAGCTCATTGCAGTTC 58.850 47.619 21.47 4.63 45.94 3.01
1786 1816 1.671742 GGGATCGGCGGTGTGATAT 59.328 57.895 7.21 0.00 0.00 1.63
1787 1817 0.892755 GGGATCGGCGGTGTGATATA 59.107 55.000 7.21 0.00 0.00 0.86
1791 1821 1.694844 TCGGCGGTGTGATATAGGAA 58.305 50.000 7.21 0.00 0.00 3.36
1792 1822 1.338973 TCGGCGGTGTGATATAGGAAC 59.661 52.381 7.21 0.00 0.00 3.62
1802 1832 6.238103 GGTGTGATATAGGAACGTGTTGATTG 60.238 42.308 0.00 0.00 0.00 2.67
1811 1841 2.408050 ACGTGTTGATTGCAGTCTCTC 58.592 47.619 10.82 4.39 0.00 3.20
2282 2318 2.231380 GGTGGTGGTGGTGGAGGAT 61.231 63.158 0.00 0.00 0.00 3.24
2438 2474 4.973055 TACCAGGTGCGCGCGTTT 62.973 61.111 32.35 11.17 0.00 3.60
2440 2476 4.622456 CCAGGTGCGCGCGTTTTT 62.622 61.111 32.35 12.41 0.00 1.94
2441 2477 3.091022 CAGGTGCGCGCGTTTTTC 61.091 61.111 32.35 14.83 0.00 2.29
2444 2480 4.322385 GTGCGCGCGTTTTTCCCT 62.322 61.111 32.35 0.00 0.00 4.20
2468 2504 1.755959 CCTCTCCCTGATGAGACTGTG 59.244 57.143 0.00 0.00 36.48 3.66
2469 2505 2.455557 CTCTCCCTGATGAGACTGTGT 58.544 52.381 0.00 0.00 36.48 3.72
2470 2506 2.166050 CTCTCCCTGATGAGACTGTGTG 59.834 54.545 0.00 0.00 36.48 3.82
2471 2507 0.610174 TCCCTGATGAGACTGTGTGC 59.390 55.000 0.00 0.00 0.00 4.57
2472 2508 0.322648 CCCTGATGAGACTGTGTGCA 59.677 55.000 0.00 0.00 0.00 4.57
2473 2509 1.065636 CCCTGATGAGACTGTGTGCAT 60.066 52.381 0.00 0.00 0.00 3.96
2474 2510 2.007608 CCTGATGAGACTGTGTGCATG 58.992 52.381 0.00 0.00 0.00 4.06
2476 2512 2.930682 CTGATGAGACTGTGTGCATGAG 59.069 50.000 0.00 0.00 0.00 2.90
2477 2513 2.301009 TGATGAGACTGTGTGCATGAGT 59.699 45.455 0.00 0.00 0.00 3.41
2518 2554 1.190833 CCAGTGCCACTCTCCAGTCT 61.191 60.000 0.00 0.00 0.00 3.24
2519 2555 0.246086 CAGTGCCACTCTCCAGTCTC 59.754 60.000 0.00 0.00 0.00 3.36
2524 2560 1.181786 CCACTCTCCAGTCTCCAGTC 58.818 60.000 0.00 0.00 0.00 3.51
2527 2563 1.272425 ACTCTCCAGTCTCCAGTCCAG 60.272 57.143 0.00 0.00 0.00 3.86
2529 2565 0.894141 CTCCAGTCTCCAGTCCAGTG 59.106 60.000 0.00 0.00 0.00 3.66
2609 2648 0.747852 GCTAGTGGTACTGGAGAGCC 59.252 60.000 0.00 0.00 0.00 4.70
2610 2649 1.025812 CTAGTGGTACTGGAGAGCCG 58.974 60.000 0.00 0.00 36.79 5.52
2611 2650 0.622136 TAGTGGTACTGGAGAGCCGA 59.378 55.000 0.00 0.00 36.79 5.54
2612 2651 0.681564 AGTGGTACTGGAGAGCCGAG 60.682 60.000 0.00 0.00 36.79 4.63
2613 2652 2.052690 TGGTACTGGAGAGCCGAGC 61.053 63.158 0.00 0.00 36.79 5.03
2614 2653 2.052690 GGTACTGGAGAGCCGAGCA 61.053 63.158 0.00 0.00 36.79 4.26
2615 2654 1.435515 GTACTGGAGAGCCGAGCAG 59.564 63.158 0.00 0.00 36.79 4.24
2708 2748 1.789506 GTGAGCTTGACTGACTGACC 58.210 55.000 0.00 0.00 28.53 4.02
2709 2749 1.069204 GTGAGCTTGACTGACTGACCA 59.931 52.381 0.00 0.00 28.53 4.02
2711 2751 2.170397 TGAGCTTGACTGACTGACCAAA 59.830 45.455 0.00 0.00 0.00 3.28
2712 2752 2.545946 GAGCTTGACTGACTGACCAAAC 59.454 50.000 0.00 0.00 0.00 2.93
2713 2753 2.092968 AGCTTGACTGACTGACCAAACA 60.093 45.455 0.00 0.00 0.00 2.83
2714 2754 2.289002 GCTTGACTGACTGACCAAACAG 59.711 50.000 0.00 0.00 42.78 3.16
2760 2800 6.042143 ACAAACAACGAGAAGAAAATGCATT 58.958 32.000 5.99 5.99 0.00 3.56
2761 2801 6.534793 ACAAACAACGAGAAGAAAATGCATTT 59.465 30.769 18.99 18.99 0.00 2.32
2762 2802 7.704472 ACAAACAACGAGAAGAAAATGCATTTA 59.296 29.630 24.35 0.00 0.00 1.40
2763 2803 7.623268 AACAACGAGAAGAAAATGCATTTAC 57.377 32.000 24.35 15.35 0.00 2.01
2764 2804 6.734137 ACAACGAGAAGAAAATGCATTTACA 58.266 32.000 24.35 0.00 0.00 2.41
2765 2805 6.857964 ACAACGAGAAGAAAATGCATTTACAG 59.142 34.615 24.35 13.57 0.00 2.74
2766 2806 5.942872 ACGAGAAGAAAATGCATTTACAGG 58.057 37.500 24.35 12.44 0.00 4.00
2767 2807 5.705441 ACGAGAAGAAAATGCATTTACAGGA 59.295 36.000 24.35 0.00 0.00 3.86
2768 2808 6.128172 ACGAGAAGAAAATGCATTTACAGGAG 60.128 38.462 24.35 15.02 0.00 3.69
2770 2810 7.064609 CGAGAAGAAAATGCATTTACAGGAGTA 59.935 37.037 24.35 0.00 0.00 2.59
2772 2812 8.897752 AGAAGAAAATGCATTTACAGGAGTATC 58.102 33.333 24.35 14.41 0.00 2.24
2773 2813 8.814038 AAGAAAATGCATTTACAGGAGTATCT 57.186 30.769 24.35 16.27 33.73 1.98
2774 2814 8.814038 AGAAAATGCATTTACAGGAGTATCTT 57.186 30.769 24.35 4.54 33.73 2.40
2775 2815 9.247861 AGAAAATGCATTTACAGGAGTATCTTT 57.752 29.630 24.35 4.09 33.73 2.52
2776 2816 9.508567 GAAAATGCATTTACAGGAGTATCTTTC 57.491 33.333 24.35 9.59 33.73 2.62
2777 2817 8.814038 AAATGCATTTACAGGAGTATCTTTCT 57.186 30.769 22.95 0.00 33.73 2.52
2778 2818 8.814038 AATGCATTTACAGGAGTATCTTTCTT 57.186 30.769 5.99 0.00 33.73 2.52
2779 2819 9.905713 AATGCATTTACAGGAGTATCTTTCTTA 57.094 29.630 5.99 0.00 33.73 2.10
2780 2820 9.905713 ATGCATTTACAGGAGTATCTTTCTTAA 57.094 29.630 0.00 0.00 33.73 1.85
2781 2821 9.162764 TGCATTTACAGGAGTATCTTTCTTAAC 57.837 33.333 0.00 0.00 33.73 2.01
2787 2830 5.970023 CAGGAGTATCTTTCTTAACGTACGG 59.030 44.000 21.06 1.09 33.73 4.02
2794 2837 3.598019 TTCTTAACGTACGGGCAGAAT 57.402 42.857 21.06 0.00 0.00 2.40
2797 2840 0.176219 TAACGTACGGGCAGAATGGG 59.824 55.000 21.06 0.00 35.86 4.00
2819 2862 3.690475 AAGACAGACACATGCTCATCA 57.310 42.857 0.00 0.00 0.00 3.07
2820 2863 3.908643 AGACAGACACATGCTCATCAT 57.091 42.857 0.00 0.00 35.31 2.45
2821 2864 3.794717 AGACAGACACATGCTCATCATC 58.205 45.455 0.00 0.00 31.79 2.92
2822 2865 2.538861 GACAGACACATGCTCATCATCG 59.461 50.000 0.00 0.00 31.79 3.84
2823 2866 2.093816 ACAGACACATGCTCATCATCGT 60.094 45.455 0.00 0.00 31.79 3.73
2972 3039 8.122472 ACACATCATCATCATCATATGCATTT 57.878 30.769 3.54 0.00 0.00 2.32
2988 3055 3.190874 GCATTTGGTTCGGACACAAAAA 58.809 40.909 12.57 1.34 37.60 1.94
3014 3081 2.167398 TTACTGGACCGAGCTGCACC 62.167 60.000 1.02 0.00 0.00 5.01
3033 3100 1.081108 GCACTGCGAGACGAGAAGT 60.081 57.895 0.00 0.00 0.00 3.01
3035 3102 1.081108 ACTGCGAGACGAGAAGTGC 60.081 57.895 0.00 0.00 0.00 4.40
3036 3103 1.211449 CTGCGAGACGAGAAGTGCT 59.789 57.895 0.00 0.00 0.00 4.40
3038 3105 0.168348 TGCGAGACGAGAAGTGCTAC 59.832 55.000 0.00 0.00 0.00 3.58
3399 3469 0.896226 AGTTCCTCTACAACCTCGGC 59.104 55.000 0.00 0.00 0.00 5.54
3476 3546 1.406898 GTCGATCAGCTCATCAGGTCA 59.593 52.381 0.00 0.00 0.00 4.02
3480 3550 1.201424 TCAGCTCATCAGGTCATGCT 58.799 50.000 0.00 0.00 0.00 3.79
3481 3551 1.138464 TCAGCTCATCAGGTCATGCTC 59.862 52.381 0.00 0.00 0.00 4.26
3482 3552 1.139256 CAGCTCATCAGGTCATGCTCT 59.861 52.381 0.00 0.00 0.00 4.09
3483 3553 1.838715 AGCTCATCAGGTCATGCTCTT 59.161 47.619 0.00 0.00 0.00 2.85
3484 3554 3.036819 AGCTCATCAGGTCATGCTCTTA 58.963 45.455 0.00 0.00 0.00 2.10
3485 3555 3.069872 AGCTCATCAGGTCATGCTCTTAG 59.930 47.826 0.00 0.00 0.00 2.18
3515 3585 2.300437 GAGCATGGATGGACCTACCTAC 59.700 54.545 0.00 0.35 39.86 3.18
3516 3586 1.348036 GCATGGATGGACCTACCTACC 59.652 57.143 0.00 0.00 39.86 3.18
3517 3587 2.977808 CATGGATGGACCTACCTACCT 58.022 52.381 8.52 0.00 39.86 3.08
3518 3588 3.757461 GCATGGATGGACCTACCTACCTA 60.757 52.174 0.00 0.00 39.86 3.08
3526 3596 5.660450 GGACCTACCTACCTAGCTCAGGG 62.660 60.870 12.18 6.50 41.45 4.45
3553 3626 4.807834 CAGTGCTGTAGTACGTAGCTACTA 59.192 45.833 21.20 6.16 39.47 1.82
3605 3682 1.500396 CGCGGCTCCTTTGTTAACC 59.500 57.895 0.00 0.00 0.00 2.85
3617 3697 5.300792 TCCTTTGTTAACCATCCTTGTCAAC 59.699 40.000 2.48 0.00 0.00 3.18
3652 3732 1.052768 GAACGTGCATGTTTCGTCGC 61.053 55.000 24.49 7.86 36.80 5.19
3691 3771 9.690434 GTGTAAATATTCTCAATCTTGTCGTTC 57.310 33.333 0.00 0.00 0.00 3.95
3717 3800 4.492791 TCATCATTTGCCATATCTTGCG 57.507 40.909 0.00 0.00 0.00 4.85
3733 3816 0.035317 TGCGTCTCTGGATTGCTTGT 59.965 50.000 0.00 0.00 0.00 3.16
3734 3817 0.445436 GCGTCTCTGGATTGCTTGTG 59.555 55.000 0.00 0.00 0.00 3.33
3735 3818 1.800805 CGTCTCTGGATTGCTTGTGT 58.199 50.000 0.00 0.00 0.00 3.72
3737 3820 2.079925 GTCTCTGGATTGCTTGTGTCC 58.920 52.381 0.00 0.00 0.00 4.02
3738 3821 1.081892 CTCTGGATTGCTTGTGTCCG 58.918 55.000 0.00 0.00 34.72 4.79
3739 3822 0.684535 TCTGGATTGCTTGTGTCCGA 59.315 50.000 0.00 0.00 34.72 4.55
3740 3823 1.081892 CTGGATTGCTTGTGTCCGAG 58.918 55.000 0.00 0.00 34.72 4.63
3741 3824 0.684535 TGGATTGCTTGTGTCCGAGA 59.315 50.000 0.00 0.00 34.72 4.04
3742 3825 1.278985 TGGATTGCTTGTGTCCGAGAT 59.721 47.619 0.00 0.00 34.72 2.75
3743 3826 1.667724 GGATTGCTTGTGTCCGAGATG 59.332 52.381 0.00 0.00 0.00 2.90
3744 3827 1.667724 GATTGCTTGTGTCCGAGATGG 59.332 52.381 0.00 0.00 40.09 3.51
3774 3857 2.125512 AGCATCGACGTGGGAAGC 60.126 61.111 0.00 0.00 0.00 3.86
3822 3908 2.676342 GGAAATTGACCTGCGAACGTAT 59.324 45.455 0.00 0.00 0.00 3.06
3823 3909 3.866910 GGAAATTGACCTGCGAACGTATA 59.133 43.478 0.00 0.00 0.00 1.47
3824 3910 4.260091 GGAAATTGACCTGCGAACGTATAC 60.260 45.833 0.00 0.00 0.00 1.47
3825 3911 1.898938 TTGACCTGCGAACGTATACG 58.101 50.000 23.24 23.24 46.33 3.06
3826 3912 1.085893 TGACCTGCGAACGTATACGA 58.914 50.000 30.77 7.83 43.02 3.43
3827 3913 1.468127 TGACCTGCGAACGTATACGAA 59.532 47.619 30.77 10.05 43.02 3.85
3844 3962 4.668576 ACGAAGTATACGAAGACACGAA 57.331 40.909 0.00 0.00 41.94 3.85
3845 3963 4.398247 ACGAAGTATACGAAGACACGAAC 58.602 43.478 0.00 0.00 41.94 3.95
3846 3964 4.083855 ACGAAGTATACGAAGACACGAACA 60.084 41.667 0.00 0.00 41.94 3.18
3847 3965 4.847757 CGAAGTATACGAAGACACGAACAA 59.152 41.667 0.00 0.00 37.03 2.83
3849 3967 4.730657 AGTATACGAAGACACGAACAAGG 58.269 43.478 0.00 0.00 37.03 3.61
3851 3969 1.567504 ACGAAGACACGAACAAGGTG 58.432 50.000 0.00 0.00 41.15 4.00
3904 4022 4.931002 GCAAGCGGGGTTCGTTATAATATA 59.069 41.667 0.00 0.00 41.72 0.86
3905 4023 5.163923 GCAAGCGGGGTTCGTTATAATATAC 60.164 44.000 0.00 0.00 41.72 1.47
3919 4070 2.928801 ATATACGCATGCACTTGGGA 57.071 45.000 19.57 0.00 34.00 4.37
3983 4145 4.143242 CGAAGCAAACAGATGAGTACTGTG 60.143 45.833 0.00 0.00 46.01 3.66
4009 4171 0.726827 CTGCAAATCATGTACGGCGT 59.273 50.000 19.64 19.64 0.00 5.68
4035 4198 4.888239 TGGTTTCTTCCCGTTCAATGTTAA 59.112 37.500 0.00 0.00 0.00 2.01
4036 4199 5.360144 TGGTTTCTTCCCGTTCAATGTTAAA 59.640 36.000 0.00 0.00 0.00 1.52
4037 4200 6.127423 TGGTTTCTTCCCGTTCAATGTTAAAA 60.127 34.615 0.00 0.00 0.00 1.52
4038 4201 6.199531 GGTTTCTTCCCGTTCAATGTTAAAAC 59.800 38.462 0.00 0.00 0.00 2.43
4040 4203 5.823353 TCTTCCCGTTCAATGTTAAAACAC 58.177 37.500 0.00 0.00 42.51 3.32
4041 4204 5.591067 TCTTCCCGTTCAATGTTAAAACACT 59.409 36.000 0.00 0.00 42.51 3.55
4042 4205 5.176407 TCCCGTTCAATGTTAAAACACTG 57.824 39.130 0.00 0.00 42.51 3.66
4043 4206 4.036971 TCCCGTTCAATGTTAAAACACTGG 59.963 41.667 4.64 0.00 42.51 4.00
4044 4207 4.202070 CCCGTTCAATGTTAAAACACTGGT 60.202 41.667 4.64 0.00 42.51 4.00
4049 4212 7.795272 CGTTCAATGTTAAAACACTGGTACTAC 59.205 37.037 4.64 0.00 42.51 2.73
4103 4266 3.617538 GTGCGTATGCTCGTCGGC 61.618 66.667 8.69 0.00 43.34 5.54
4104 4267 3.822192 TGCGTATGCTCGTCGGCT 61.822 61.111 8.69 0.00 43.34 5.52
4105 4268 3.025176 GCGTATGCTCGTCGGCTC 61.025 66.667 0.00 0.00 38.39 4.70
4106 4269 2.722548 CGTATGCTCGTCGGCTCG 60.723 66.667 7.14 5.97 0.00 5.03
4107 4270 2.408022 GTATGCTCGTCGGCTCGT 59.592 61.111 7.14 0.00 0.00 4.18
4108 4271 1.939785 GTATGCTCGTCGGCTCGTG 60.940 63.158 7.14 0.00 0.00 4.35
4109 4272 2.110352 TATGCTCGTCGGCTCGTGA 61.110 57.895 7.14 0.00 0.00 4.35
4110 4273 2.048312 TATGCTCGTCGGCTCGTGAG 62.048 60.000 7.14 11.82 35.14 3.51
4111 4274 4.838486 GCTCGTCGGCTCGTGAGG 62.838 72.222 15.25 3.40 33.67 3.86
4123 4292 2.202810 GTGAGGCGCTGCTAGACC 60.203 66.667 7.64 0.00 0.00 3.85
4152 4321 0.179240 CACTTTCTCATCACGTGCGC 60.179 55.000 11.67 0.00 0.00 6.09
4153 4322 1.291877 ACTTTCTCATCACGTGCGCC 61.292 55.000 11.67 0.00 0.00 6.53
4154 4323 1.005037 TTTCTCATCACGTGCGCCT 60.005 52.632 11.67 0.00 0.00 5.52
4155 4324 1.014044 TTTCTCATCACGTGCGCCTC 61.014 55.000 11.67 0.00 0.00 4.70
4167 4336 4.085302 CGCCTCGCAGAAGAGAAG 57.915 61.111 0.00 0.00 40.57 2.85
4168 4337 1.518133 CGCCTCGCAGAAGAGAAGG 60.518 63.158 0.00 0.00 40.57 3.46
4169 4338 1.594310 GCCTCGCAGAAGAGAAGGT 59.406 57.895 0.00 0.00 40.57 3.50
4171 4340 0.891373 CCTCGCAGAAGAGAAGGTGA 59.109 55.000 0.00 0.00 40.57 4.02
4174 4351 1.964223 TCGCAGAAGAGAAGGTGAGTT 59.036 47.619 0.00 0.00 0.00 3.01
4209 4386 1.734137 CCGATCAGTACCACCTCCG 59.266 63.158 0.00 0.00 0.00 4.63
4211 4388 0.100682 CGATCAGTACCACCTCCGTG 59.899 60.000 0.00 0.00 39.91 4.94
4241 4418 2.669391 GCAAAGCTACAAGCATGGACAC 60.669 50.000 1.22 0.00 45.56 3.67
4242 4419 1.826385 AAGCTACAAGCATGGACACC 58.174 50.000 1.22 0.00 45.56 4.16
4243 4420 0.692476 AGCTACAAGCATGGACACCA 59.308 50.000 1.22 0.00 45.56 4.17
4244 4421 1.073763 AGCTACAAGCATGGACACCAA 59.926 47.619 1.22 0.00 45.56 3.67
4245 4422 1.470098 GCTACAAGCATGGACACCAAG 59.530 52.381 0.00 0.00 41.89 3.61
4249 4426 2.173519 CAAGCATGGACACCAAGGAAT 58.826 47.619 0.00 0.00 36.95 3.01
4255 4432 2.170166 TGGACACCAAGGAATGAATGC 58.830 47.619 0.00 0.00 0.00 3.56
4285 4469 1.424493 GACGTACATGGCTCAGCAGC 61.424 60.000 0.00 0.00 46.06 5.25
4321 4505 3.103007 GTCGTTCAAAGTTTCAAACCGG 58.897 45.455 0.00 0.00 0.00 5.28
4322 4506 3.008330 TCGTTCAAAGTTTCAAACCGGA 58.992 40.909 9.46 0.00 0.00 5.14
4346 4530 3.067106 CAGTGTGTGTATGTGTTCTCCC 58.933 50.000 0.00 0.00 0.00 4.30
4355 4539 0.031585 TGTGTTCTCCCGACGAACTG 59.968 55.000 0.00 0.00 40.95 3.16
4362 4546 0.038892 TCCCGACGAACTGCAGTAAC 60.039 55.000 22.01 16.07 0.00 2.50
4368 4552 2.201732 ACGAACTGCAGTAACACAGTG 58.798 47.619 22.01 0.00 46.17 3.66
4373 4557 2.168521 ACTGCAGTAACACAGTGACACT 59.831 45.455 20.16 1.07 45.19 3.55
4374 4558 3.383505 ACTGCAGTAACACAGTGACACTA 59.616 43.478 20.16 0.00 45.19 2.74
4375 4559 3.977427 TGCAGTAACACAGTGACACTAG 58.023 45.455 8.02 6.73 0.00 2.57
4376 4560 3.243737 TGCAGTAACACAGTGACACTAGG 60.244 47.826 8.02 5.97 0.00 3.02
4377 4561 3.005472 GCAGTAACACAGTGACACTAGGA 59.995 47.826 8.02 0.00 0.00 2.94
4385 4572 1.286553 AGTGACACTAGGAGGGAGAGG 59.713 57.143 6.24 0.00 0.00 3.69
4386 4573 0.631753 TGACACTAGGAGGGAGAGGG 59.368 60.000 0.00 0.00 0.00 4.30
4395 4590 1.222567 GAGGGAGAGGGAGAGAGAGT 58.777 60.000 0.00 0.00 0.00 3.24
4400 4595 2.158755 GGAGAGGGAGAGAGAGTGAGAG 60.159 59.091 0.00 0.00 0.00 3.20
4408 4603 4.876107 GGAGAGAGAGTGAGAGAACAGTAG 59.124 50.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.589159 TTACGCAGTGCCGTGCAA 60.589 55.556 18.62 6.93 45.73 4.08
18 19 1.076533 CCACTACTTACGCAGTGCCG 61.077 60.000 10.11 7.47 45.73 5.69
23 24 3.476295 TCGTAACCACTACTTACGCAG 57.524 47.619 5.96 0.00 43.96 5.18
28 29 4.260985 TCACGGATCGTAACCACTACTTA 58.739 43.478 0.00 0.00 38.32 2.24
29 30 3.084039 TCACGGATCGTAACCACTACTT 58.916 45.455 0.00 0.00 38.32 2.24
30 31 2.715046 TCACGGATCGTAACCACTACT 58.285 47.619 0.00 0.00 38.32 2.57
31 32 3.549625 GGATCACGGATCGTAACCACTAC 60.550 52.174 0.00 0.00 39.72 2.73
39 40 2.160205 GGAGATGGATCACGGATCGTA 58.840 52.381 0.00 1.70 39.72 3.43
60 61 4.685169 AAACATCCAGAAACATGCTACG 57.315 40.909 0.00 0.00 0.00 3.51
71 72 1.339631 CCTACCCGCAAAACATCCAGA 60.340 52.381 0.00 0.00 0.00 3.86
81 82 5.172205 GCAAATTAAAATTCCTACCCGCAA 58.828 37.500 0.00 0.00 0.00 4.85
94 95 3.293262 GTGCGTCGACTGCAAATTAAAA 58.707 40.909 27.78 8.16 45.23 1.52
101 102 2.089887 TTAGGGTGCGTCGACTGCAA 62.090 55.000 27.78 15.19 45.23 4.08
102 103 2.566570 TTAGGGTGCGTCGACTGCA 61.567 57.895 24.25 24.25 40.70 4.41
120 121 7.120923 AGATATGTAATGTTGGGTTCTACGT 57.879 36.000 0.00 0.00 0.00 3.57
121 122 7.926555 AGAAGATATGTAATGTTGGGTTCTACG 59.073 37.037 0.00 0.00 0.00 3.51
154 155 9.696572 AGGAACACTAGAACATACATAAGTAGA 57.303 33.333 0.00 0.00 32.86 2.59
161 162 4.441634 GGCGAGGAACACTAGAACATACAT 60.442 45.833 0.00 0.00 0.00 2.29
173 174 2.737376 GTCACCGGCGAGGAACAC 60.737 66.667 9.30 0.00 45.00 3.32
174 175 3.998672 GGTCACCGGCGAGGAACA 61.999 66.667 9.30 0.00 45.00 3.18
206 207 2.707039 CGGCGGCGATAAAACCTG 59.293 61.111 29.19 0.00 0.00 4.00
207 208 3.199891 GCGGCGGCGATAAAACCT 61.200 61.111 36.87 0.00 0.00 3.50
229 230 3.917760 CCTCCATCCGCCGTCTCC 61.918 72.222 0.00 0.00 0.00 3.71
259 260 4.755629 GTCTAAGTCCTTGTTGTTCCCTTC 59.244 45.833 0.00 0.00 0.00 3.46
288 289 3.207669 CCTAGACTACGGCGGCGT 61.208 66.667 38.68 38.68 0.00 5.68
292 293 2.019984 ACCTAAACCTAGACTACGGCG 58.980 52.381 4.80 4.80 0.00 6.46
317 318 8.950007 AGATAGTTTTCATTAACAAAAGGGGA 57.050 30.769 0.00 0.00 0.00 4.81
337 338 7.024340 AGCACATTCACTGCATTTTAGATAG 57.976 36.000 0.00 0.00 37.08 2.08
339 340 5.163581 GGAGCACATTCACTGCATTTTAGAT 60.164 40.000 0.00 0.00 37.08 1.98
342 343 3.119884 CGGAGCACATTCACTGCATTTTA 60.120 43.478 0.00 0.00 37.08 1.52
343 344 2.352030 CGGAGCACATTCACTGCATTTT 60.352 45.455 0.00 0.00 37.08 1.82
349 350 2.033299 ACAAAACGGAGCACATTCACTG 59.967 45.455 0.00 0.00 0.00 3.66
389 390 2.489329 ACCAACTGAGCGAAAATCATGG 59.511 45.455 0.00 0.00 34.41 3.66
395 396 3.191581 TGTTTCAACCAACTGAGCGAAAA 59.808 39.130 0.00 0.00 0.00 2.29
399 400 1.670811 AGTGTTTCAACCAACTGAGCG 59.329 47.619 0.00 0.00 0.00 5.03
401 402 5.584649 TCAAGTAGTGTTTCAACCAACTGAG 59.415 40.000 0.00 0.00 0.00 3.35
404 405 6.827586 TTTCAAGTAGTGTTTCAACCAACT 57.172 33.333 0.00 0.00 0.00 3.16
417 418 8.492415 TGCTATCCCTATACATTTCAAGTAGT 57.508 34.615 0.00 0.00 0.00 2.73
421 422 9.725019 TGTTATGCTATCCCTATACATTTCAAG 57.275 33.333 0.00 0.00 0.00 3.02
434 435 5.106555 CGGTCATTCAATGTTATGCTATCCC 60.107 44.000 0.00 0.00 0.00 3.85
441 442 5.511377 CGAAAACCGGTCATTCAATGTTATG 59.489 40.000 24.56 8.88 33.91 1.90
442 443 5.182380 ACGAAAACCGGTCATTCAATGTTAT 59.818 36.000 24.56 0.00 43.93 1.89
443 444 4.515944 ACGAAAACCGGTCATTCAATGTTA 59.484 37.500 24.56 0.00 43.93 2.41
444 445 3.316868 ACGAAAACCGGTCATTCAATGTT 59.683 39.130 24.56 5.41 43.93 2.71
445 446 2.882137 ACGAAAACCGGTCATTCAATGT 59.118 40.909 24.56 15.52 43.93 2.71
446 447 3.552604 ACGAAAACCGGTCATTCAATG 57.447 42.857 24.56 15.04 43.93 2.82
451 452 7.095270 GGATATAGATACGAAAACCGGTCATT 58.905 38.462 8.04 6.39 43.93 2.57
462 463 5.554070 TCTGTCCACGGATATAGATACGAA 58.446 41.667 9.37 0.00 42.51 3.85
463 464 5.156608 TCTGTCCACGGATATAGATACGA 57.843 43.478 9.37 0.00 42.51 3.43
466 467 6.719829 ACAACATCTGTCCACGGATATAGATA 59.280 38.462 0.54 0.00 39.82 1.98
471 472 3.197766 ACACAACATCTGTCCACGGATAT 59.802 43.478 0.54 0.00 39.82 1.63
482 483 3.126858 CCATAAACCGGACACAACATCTG 59.873 47.826 9.46 0.00 0.00 2.90
487 488 1.808343 GACCCATAAACCGGACACAAC 59.192 52.381 9.46 0.00 0.00 3.32
489 490 1.002659 CTGACCCATAAACCGGACACA 59.997 52.381 9.46 0.00 0.00 3.72
504 505 1.883021 CGCATTTCCAACCCTGACC 59.117 57.895 0.00 0.00 0.00 4.02
549 550 0.032540 GGCTTTGTTTCTGTGCCTGG 59.967 55.000 0.00 0.00 40.36 4.45
591 592 1.945580 TTAAAGGGGGATGTTTGGGC 58.054 50.000 0.00 0.00 0.00 5.36
602 603 1.310216 CCTTCGCCGGTTTAAAGGGG 61.310 60.000 1.90 5.94 41.23 4.79
616 617 2.551032 GGTTTTAGTTGGTGTCCCTTCG 59.449 50.000 0.00 0.00 0.00 3.79
631 632 3.339547 GGCAGAGCCTGTGGTTTTA 57.660 52.632 0.00 0.00 46.69 1.52
752 756 3.562108 ATGGACTTACGGGGGAGATAT 57.438 47.619 0.00 0.00 0.00 1.63
753 757 4.474303 TTATGGACTTACGGGGGAGATA 57.526 45.455 0.00 0.00 0.00 1.98
754 758 3.339713 TTATGGACTTACGGGGGAGAT 57.660 47.619 0.00 0.00 0.00 2.75
755 759 2.767960 GTTTATGGACTTACGGGGGAGA 59.232 50.000 0.00 0.00 0.00 3.71
756 760 2.502538 TGTTTATGGACTTACGGGGGAG 59.497 50.000 0.00 0.00 0.00 4.30
757 761 2.549082 TGTTTATGGACTTACGGGGGA 58.451 47.619 0.00 0.00 0.00 4.81
758 762 3.353370 TTGTTTATGGACTTACGGGGG 57.647 47.619 0.00 0.00 0.00 5.40
759 763 8.857694 ATATATTTGTTTATGGACTTACGGGG 57.142 34.615 0.00 0.00 0.00 5.73
810 814 9.562408 GCAGCTCACCTAGTCATAGTATATATA 57.438 37.037 0.00 0.00 0.00 0.86
811 815 8.278639 AGCAGCTCACCTAGTCATAGTATATAT 58.721 37.037 0.00 0.00 0.00 0.86
812 816 7.634718 AGCAGCTCACCTAGTCATAGTATATA 58.365 38.462 0.00 0.00 0.00 0.86
821 825 1.547820 CTGAAGCAGCTCACCTAGTCA 59.452 52.381 0.00 0.00 0.00 3.41
846 850 2.808543 CCCTGTTGCTGTTTGTACTCTC 59.191 50.000 0.00 0.00 0.00 3.20
1090 1117 1.177401 GAGGAAGAACATGGGGTTGC 58.823 55.000 0.00 0.00 40.63 4.17
1119 1146 0.478507 AAGGGACACAGGTCAAAGGG 59.521 55.000 0.00 0.00 46.17 3.95
1130 1157 2.290641 CAGCACAGTTAACAAGGGACAC 59.709 50.000 8.61 0.00 0.00 3.67
1470 1497 0.322277 AGACAGGGATGCTGCAAGTG 60.322 55.000 6.36 4.42 35.30 3.16
1473 1500 0.609957 CCAAGACAGGGATGCTGCAA 60.610 55.000 6.36 0.00 0.00 4.08
1518 1545 2.599659 CCCAAATCGAAAGCAGAAAGC 58.400 47.619 0.00 0.00 46.19 3.51
1657 1685 6.315642 GGGATTCTTTGTAGTACTTTACCTGC 59.684 42.308 0.00 0.00 0.00 4.85
1672 1700 0.529378 GCACAGGCTGGGATTCTTTG 59.471 55.000 23.56 7.04 36.96 2.77
1736 1764 1.290491 GCTCACACTCTGCTCTGCAC 61.290 60.000 0.00 0.00 33.79 4.57
1746 1774 1.805869 ACTGCAATGAGCTCACACTC 58.194 50.000 20.97 9.23 45.94 3.51
1747 1775 2.149578 GAACTGCAATGAGCTCACACT 58.850 47.619 20.97 3.49 45.94 3.55
1748 1776 1.136141 CGAACTGCAATGAGCTCACAC 60.136 52.381 20.97 11.97 45.94 3.82
1767 1797 2.154798 ATATCACACCGCCGATCCCG 62.155 60.000 0.00 0.00 0.00 5.14
1778 1808 6.705782 CAATCAACACGTTCCTATATCACAC 58.294 40.000 0.00 0.00 0.00 3.82
1786 1816 3.064207 GACTGCAATCAACACGTTCCTA 58.936 45.455 0.00 0.00 0.00 2.94
1787 1817 1.873591 GACTGCAATCAACACGTTCCT 59.126 47.619 0.00 0.00 0.00 3.36
1791 1821 2.408050 GAGAGACTGCAATCAACACGT 58.592 47.619 0.00 0.00 0.00 4.49
1792 1822 1.388093 CGAGAGACTGCAATCAACACG 59.612 52.381 0.00 0.00 0.00 4.49
1802 1832 4.200283 CCGGCTCCGAGAGACTGC 62.200 72.222 10.28 0.00 42.83 4.40
2063 2093 2.338620 CGCTTCACCGTGTCCAGA 59.661 61.111 0.00 0.00 0.00 3.86
2365 2401 0.450583 GACGAGGTACTGCATGTCGA 59.549 55.000 6.63 0.00 41.55 4.20
2436 2472 2.644798 CAGGGAGAGGAGAAGGGAAAAA 59.355 50.000 0.00 0.00 0.00 1.94
2437 2473 2.158004 TCAGGGAGAGGAGAAGGGAAAA 60.158 50.000 0.00 0.00 0.00 2.29
2438 2474 1.437149 TCAGGGAGAGGAGAAGGGAAA 59.563 52.381 0.00 0.00 0.00 3.13
2440 2476 1.062581 CATCAGGGAGAGGAGAAGGGA 60.063 57.143 0.00 0.00 0.00 4.20
2441 2477 1.062581 TCATCAGGGAGAGGAGAAGGG 60.063 57.143 0.00 0.00 30.96 3.95
2471 2507 5.481200 AAAGAAAGATGCATCGACTCATG 57.519 39.130 20.67 0.00 0.00 3.07
2472 2508 4.574013 GGAAAGAAAGATGCATCGACTCAT 59.426 41.667 20.67 12.79 0.00 2.90
2473 2509 3.935203 GGAAAGAAAGATGCATCGACTCA 59.065 43.478 20.67 0.00 0.00 3.41
2474 2510 3.311048 GGGAAAGAAAGATGCATCGACTC 59.689 47.826 20.67 17.01 0.00 3.36
2476 2512 3.064545 CAGGGAAAGAAAGATGCATCGAC 59.935 47.826 20.67 15.13 0.00 4.20
2477 2513 3.273434 CAGGGAAAGAAAGATGCATCGA 58.727 45.455 20.67 0.00 0.00 3.59
2518 2554 1.771783 ATGCTGTGCACTGGACTGGA 61.772 55.000 23.15 6.92 43.04 3.86
2519 2555 0.892358 AATGCTGTGCACTGGACTGG 60.892 55.000 23.15 4.56 43.04 4.00
2524 2560 1.603678 GGTGAAAATGCTGTGCACTGG 60.604 52.381 23.15 14.51 43.04 4.00
2527 2563 0.664166 CCGGTGAAAATGCTGTGCAC 60.664 55.000 10.75 10.75 43.04 4.57
2529 2565 0.031994 AACCGGTGAAAATGCTGTGC 59.968 50.000 8.52 0.00 0.00 4.57
2609 2648 0.595567 GCATCTCTGCTCTCTGCTCG 60.596 60.000 0.00 0.00 45.32 5.03
2610 2649 3.277652 GCATCTCTGCTCTCTGCTC 57.722 57.895 0.00 0.00 45.32 4.26
2708 2748 2.222027 AGGAACGAAAGGAGCTGTTTG 58.778 47.619 0.00 0.00 0.00 2.93
2709 2749 2.640316 AGGAACGAAAGGAGCTGTTT 57.360 45.000 0.00 0.00 0.00 2.83
2711 2751 3.181489 CGTATAGGAACGAAAGGAGCTGT 60.181 47.826 0.00 0.00 45.68 4.40
2712 2752 3.372954 CGTATAGGAACGAAAGGAGCTG 58.627 50.000 0.00 0.00 45.68 4.24
2713 2753 2.223758 GCGTATAGGAACGAAAGGAGCT 60.224 50.000 0.00 0.00 45.68 4.09
2714 2754 2.125685 GCGTATAGGAACGAAAGGAGC 58.874 52.381 0.00 0.00 45.68 4.70
2760 2800 8.177663 CGTACGTTAAGAAAGATACTCCTGTAA 58.822 37.037 7.22 0.00 31.80 2.41
2761 2801 7.201644 CCGTACGTTAAGAAAGATACTCCTGTA 60.202 40.741 15.21 0.00 0.00 2.74
2762 2802 6.404074 CCGTACGTTAAGAAAGATACTCCTGT 60.404 42.308 15.21 0.00 0.00 4.00
2763 2803 5.970023 CCGTACGTTAAGAAAGATACTCCTG 59.030 44.000 15.21 0.00 0.00 3.86
2764 2804 5.067023 CCCGTACGTTAAGAAAGATACTCCT 59.933 44.000 15.21 0.00 0.00 3.69
2765 2805 5.277047 CCCGTACGTTAAGAAAGATACTCC 58.723 45.833 15.21 0.00 0.00 3.85
2766 2806 4.737279 GCCCGTACGTTAAGAAAGATACTC 59.263 45.833 15.21 0.00 0.00 2.59
2767 2807 4.158394 TGCCCGTACGTTAAGAAAGATACT 59.842 41.667 15.21 0.00 0.00 2.12
2768 2808 4.423732 TGCCCGTACGTTAAGAAAGATAC 58.576 43.478 15.21 0.00 0.00 2.24
2770 2810 3.194116 TCTGCCCGTACGTTAAGAAAGAT 59.806 43.478 15.21 0.00 0.00 2.40
2772 2812 2.950433 TCTGCCCGTACGTTAAGAAAG 58.050 47.619 15.21 2.17 0.00 2.62
2773 2813 3.383620 TTCTGCCCGTACGTTAAGAAA 57.616 42.857 15.21 0.00 0.00 2.52
2774 2814 3.255725 CATTCTGCCCGTACGTTAAGAA 58.744 45.455 19.51 19.51 0.00 2.52
2775 2815 2.417651 CCATTCTGCCCGTACGTTAAGA 60.418 50.000 15.21 10.38 0.00 2.10
2776 2816 1.931172 CCATTCTGCCCGTACGTTAAG 59.069 52.381 15.21 8.15 0.00 1.85
2777 2817 1.405797 CCCATTCTGCCCGTACGTTAA 60.406 52.381 15.21 1.24 0.00 2.01
2778 2818 0.176219 CCCATTCTGCCCGTACGTTA 59.824 55.000 15.21 0.00 0.00 3.18
2779 2819 1.078708 CCCATTCTGCCCGTACGTT 60.079 57.895 15.21 0.00 0.00 3.99
2780 2820 1.546589 TTCCCATTCTGCCCGTACGT 61.547 55.000 15.21 0.00 0.00 3.57
2781 2821 0.391927 TTTCCCATTCTGCCCGTACG 60.392 55.000 8.69 8.69 0.00 3.67
2787 2830 2.087646 GTCTGTCTTTCCCATTCTGCC 58.912 52.381 0.00 0.00 0.00 4.85
2794 2837 1.421268 AGCATGTGTCTGTCTTTCCCA 59.579 47.619 0.00 0.00 0.00 4.37
2797 2840 3.999001 TGATGAGCATGTGTCTGTCTTTC 59.001 43.478 0.00 0.00 0.00 2.62
2819 2862 3.082579 GCAGGAGCGGAGGAACGAT 62.083 63.158 0.00 0.00 35.47 3.73
2820 2863 3.760035 GCAGGAGCGGAGGAACGA 61.760 66.667 0.00 0.00 35.47 3.85
2821 2864 4.069232 TGCAGGAGCGGAGGAACG 62.069 66.667 0.00 0.00 46.23 3.95
2988 3055 2.567615 AGCTCGGTCCAGTAAGAATGTT 59.432 45.455 0.00 0.00 0.00 2.71
2989 3056 2.093973 CAGCTCGGTCCAGTAAGAATGT 60.094 50.000 0.00 0.00 0.00 2.71
3021 3088 3.206348 CGTAGCACTTCTCGTCTCG 57.794 57.895 0.00 0.00 0.00 4.04
3043 3113 2.252260 GCAAACGCGTCACATGCT 59.748 55.556 23.36 2.14 34.29 3.79
3286 3356 2.266055 GGCGTCCTCCTTGACCAG 59.734 66.667 0.00 0.00 31.35 4.00
3399 3469 3.640498 TCTAAGAGCATGACCTGATGAGG 59.360 47.826 0.00 0.00 46.21 3.86
3427 3497 1.200519 GTGGTAGGTAGGTCCATGCA 58.799 55.000 0.00 0.00 39.02 3.96
3428 3498 0.468648 GGTGGTAGGTAGGTCCATGC 59.531 60.000 0.00 0.00 39.02 4.06
3429 3499 2.176247 AGGTGGTAGGTAGGTCCATG 57.824 55.000 0.00 0.00 39.02 3.66
3480 3550 5.130705 TCCATGCTCCTCTAAGACTAAGA 57.869 43.478 0.00 0.00 0.00 2.10
3481 3551 5.279406 CCATCCATGCTCCTCTAAGACTAAG 60.279 48.000 0.00 0.00 0.00 2.18
3482 3552 4.590647 CCATCCATGCTCCTCTAAGACTAA 59.409 45.833 0.00 0.00 0.00 2.24
3483 3553 4.140924 TCCATCCATGCTCCTCTAAGACTA 60.141 45.833 0.00 0.00 0.00 2.59
3484 3554 2.971330 CCATCCATGCTCCTCTAAGACT 59.029 50.000 0.00 0.00 0.00 3.24
3485 3555 2.968574 TCCATCCATGCTCCTCTAAGAC 59.031 50.000 0.00 0.00 0.00 3.01
3515 3585 0.392193 CACTGCAACCCTGAGCTAGG 60.392 60.000 0.00 0.00 46.88 3.02
3516 3586 1.023513 GCACTGCAACCCTGAGCTAG 61.024 60.000 0.00 0.00 0.00 3.42
3517 3587 1.003355 GCACTGCAACCCTGAGCTA 60.003 57.895 0.00 0.00 0.00 3.32
3518 3588 2.282040 GCACTGCAACCCTGAGCT 60.282 61.111 0.00 0.00 0.00 4.09
3526 3596 1.779569 ACGTACTACAGCACTGCAAC 58.220 50.000 3.30 0.00 0.00 4.17
3601 3678 5.070001 CCAAGAAGTTGACAAGGATGGTTA 58.930 41.667 0.00 0.00 35.46 2.85
3605 3682 3.254166 CACCCAAGAAGTTGACAAGGATG 59.746 47.826 0.00 0.00 35.46 3.51
3617 3697 2.949644 ACGTTCCTTTTCACCCAAGAAG 59.050 45.455 0.00 0.00 0.00 2.85
3652 3732 8.668510 AGAATATTTACACTGCTACTGATTGG 57.331 34.615 0.00 0.00 0.00 3.16
3691 3771 6.641314 GCAAGATATGGCAAATGATGAAGAAG 59.359 38.462 0.00 0.00 0.00 2.85
3717 3800 2.079925 GGACACAAGCAATCCAGAGAC 58.920 52.381 0.00 0.00 32.35 3.36
3735 3818 2.415608 GCGGACAGTCCATCTCGGA 61.416 63.158 20.13 0.00 43.61 4.55
3737 3820 2.278206 CGCGGACAGTCCATCTCG 60.278 66.667 20.13 12.31 35.91 4.04
3738 3821 1.226717 GACGCGGACAGTCCATCTC 60.227 63.158 20.13 6.07 35.91 2.75
3739 3822 1.938657 CTGACGCGGACAGTCCATCT 61.939 60.000 20.13 0.00 35.91 2.90
3740 3823 1.517257 CTGACGCGGACAGTCCATC 60.517 63.158 20.13 13.41 35.91 3.51
3741 3824 2.573869 CTGACGCGGACAGTCCAT 59.426 61.111 20.13 4.00 35.91 3.41
3742 3825 4.357947 GCTGACGCGGACAGTCCA 62.358 66.667 26.90 0.00 35.91 4.02
3743 3826 3.649277 ATGCTGACGCGGACAGTCC 62.649 63.158 26.90 9.92 39.65 3.85
3744 3827 2.125912 ATGCTGACGCGGACAGTC 60.126 61.111 26.90 21.16 39.65 3.51
3774 3857 5.396484 TCTCGTGATTCGTGGTTAACTTAG 58.604 41.667 5.42 0.00 40.80 2.18
3822 3908 5.120053 TGTTCGTGTCTTCGTATACTTCGTA 59.880 40.000 0.56 0.00 0.00 3.43
3823 3909 4.083855 TGTTCGTGTCTTCGTATACTTCGT 60.084 41.667 0.56 0.00 0.00 3.85
3824 3910 4.397382 TGTTCGTGTCTTCGTATACTTCG 58.603 43.478 0.56 0.00 0.00 3.79
3825 3911 5.285607 CCTTGTTCGTGTCTTCGTATACTTC 59.714 44.000 0.56 0.00 0.00 3.01
3826 3912 5.159209 CCTTGTTCGTGTCTTCGTATACTT 58.841 41.667 0.56 0.00 0.00 2.24
3827 3913 4.217118 ACCTTGTTCGTGTCTTCGTATACT 59.783 41.667 0.56 0.00 0.00 2.12
3840 3958 0.732880 CTCGATCGCACCTTGTTCGT 60.733 55.000 11.09 0.00 0.00 3.85
3842 3960 0.389948 ACCTCGATCGCACCTTGTTC 60.390 55.000 11.09 0.00 0.00 3.18
3844 3962 1.215647 GACCTCGATCGCACCTTGT 59.784 57.895 11.09 0.50 0.00 3.16
3845 3963 1.519455 GGACCTCGATCGCACCTTG 60.519 63.158 11.09 0.00 0.00 3.61
3846 3964 1.258445 AAGGACCTCGATCGCACCTT 61.258 55.000 20.37 20.37 33.66 3.50
3847 3965 1.682684 AAGGACCTCGATCGCACCT 60.683 57.895 11.09 12.56 0.00 4.00
3849 3967 1.078759 CACAAGGACCTCGATCGCAC 61.079 60.000 11.09 1.30 0.00 5.34
3851 3969 2.167861 GCACAAGGACCTCGATCGC 61.168 63.158 11.09 0.00 0.00 4.58
3875 3993 0.168128 CGAACCCCGCTTGCTTTAAG 59.832 55.000 0.00 0.00 39.49 1.85
3904 4022 3.049674 CGTCCCAAGTGCATGCGT 61.050 61.111 14.09 0.00 0.00 5.24
3905 4023 3.803082 CCGTCCCAAGTGCATGCG 61.803 66.667 14.09 0.00 0.00 4.73
3919 4070 1.416243 TTTGACACCACCTAGACCGT 58.584 50.000 0.00 0.00 0.00 4.83
3982 4144 5.391843 CCGTACATGATTTGCAGTTGAATCA 60.392 40.000 12.63 12.63 43.91 2.57
3983 4145 5.030295 CCGTACATGATTTGCAGTTGAATC 58.970 41.667 0.00 2.48 33.83 2.52
4009 4171 3.284793 TTGAACGGGAAGAAACCAAGA 57.715 42.857 0.00 0.00 0.00 3.02
4068 4231 2.161410 GCACGCATTGATGAAAGGTACA 59.839 45.455 0.00 0.00 0.00 2.90
4071 4234 0.168788 CGCACGCATTGATGAAAGGT 59.831 50.000 0.00 0.00 0.00 3.50
4076 4239 0.304401 GCATACGCACGCATTGATGA 59.696 50.000 0.00 0.00 38.36 2.92
4077 4240 0.305617 AGCATACGCACGCATTGATG 59.694 50.000 0.00 0.00 42.27 3.07
4078 4241 0.583438 GAGCATACGCACGCATTGAT 59.417 50.000 0.00 0.00 42.27 2.57
4106 4269 2.202810 GGTCTAGCAGCGCCTCAC 60.203 66.667 2.29 0.00 0.00 3.51
4107 4270 2.679996 TGGTCTAGCAGCGCCTCA 60.680 61.111 2.29 0.00 0.00 3.86
4108 4271 2.202810 GTGGTCTAGCAGCGCCTC 60.203 66.667 2.29 0.00 0.00 4.70
4109 4272 2.681778 AGTGGTCTAGCAGCGCCT 60.682 61.111 2.29 0.00 33.10 5.52
4110 4273 2.510238 CAGTGGTCTAGCAGCGCC 60.510 66.667 2.29 0.00 33.10 6.53
4111 4274 1.518133 CTCAGTGGTCTAGCAGCGC 60.518 63.158 0.00 0.00 0.00 5.92
4112 4275 1.140589 CCTCAGTGGTCTAGCAGCG 59.859 63.158 0.00 0.00 0.00 5.18
4123 4292 4.450419 GTGATGAGAAAGTGAACCTCAGTG 59.550 45.833 0.00 0.00 39.89 3.66
4133 4302 0.179240 GCGCACGTGATGAGAAAGTG 60.179 55.000 22.23 0.00 36.05 3.16
4139 4308 3.250323 CGAGGCGCACGTGATGAG 61.250 66.667 22.23 8.06 0.00 2.90
4152 4321 0.891373 TCACCTTCTCTTCTGCGAGG 59.109 55.000 0.00 0.00 0.00 4.63
4153 4322 1.543802 ACTCACCTTCTCTTCTGCGAG 59.456 52.381 0.00 0.00 0.00 5.03
4154 4323 1.621992 ACTCACCTTCTCTTCTGCGA 58.378 50.000 0.00 0.00 0.00 5.10
4155 4324 2.447244 AACTCACCTTCTCTTCTGCG 57.553 50.000 0.00 0.00 0.00 5.18
4157 4326 7.659390 AGTTGAATTAACTCACCTTCTCTTCTG 59.341 37.037 0.00 0.00 46.55 3.02
4158 4327 7.659390 CAGTTGAATTAACTCACCTTCTCTTCT 59.341 37.037 0.00 0.00 46.55 2.85
4160 4329 6.205658 GCAGTTGAATTAACTCACCTTCTCTT 59.794 38.462 0.00 0.00 46.55 2.85
4161 4330 5.703130 GCAGTTGAATTAACTCACCTTCTCT 59.297 40.000 0.00 0.00 46.55 3.10
4163 4332 4.762251 GGCAGTTGAATTAACTCACCTTCT 59.238 41.667 0.00 0.00 46.55 2.85
4164 4333 4.378459 CGGCAGTTGAATTAACTCACCTTC 60.378 45.833 5.39 0.00 46.55 3.46
4165 4334 3.502211 CGGCAGTTGAATTAACTCACCTT 59.498 43.478 5.39 0.00 46.55 3.50
4166 4335 3.074412 CGGCAGTTGAATTAACTCACCT 58.926 45.455 5.39 0.00 46.55 4.00
4167 4336 2.812011 ACGGCAGTTGAATTAACTCACC 59.188 45.455 0.00 0.00 46.55 4.02
4168 4337 4.464112 GAACGGCAGTTGAATTAACTCAC 58.536 43.478 7.05 0.00 46.55 3.51
4169 4338 3.500680 GGAACGGCAGTTGAATTAACTCA 59.499 43.478 7.05 0.00 46.55 3.41
4232 4409 1.838112 TCATTCCTTGGTGTCCATGC 58.162 50.000 0.00 0.00 31.53 4.06
4241 4418 2.093921 TGTGCATGCATTCATTCCTTGG 60.094 45.455 25.64 0.00 0.00 3.61
4242 4419 2.927477 GTGTGCATGCATTCATTCCTTG 59.073 45.455 25.64 0.00 0.00 3.61
4243 4420 2.416296 CGTGTGCATGCATTCATTCCTT 60.416 45.455 25.64 0.00 0.00 3.36
4244 4421 1.133598 CGTGTGCATGCATTCATTCCT 59.866 47.619 25.64 0.00 0.00 3.36
4245 4422 1.132834 TCGTGTGCATGCATTCATTCC 59.867 47.619 25.64 9.55 0.00 3.01
4249 4426 0.798159 GTCTCGTGTGCATGCATTCA 59.202 50.000 25.64 15.56 0.00 2.57
4255 4432 1.321445 CATGTACGTCTCGTGTGCATG 59.679 52.381 9.21 9.21 41.39 4.06
4285 4469 3.869272 GACGCGCTTCTGCCATGG 61.869 66.667 7.63 7.63 35.36 3.66
4300 4484 3.103007 CCGGTTTGAAACTTTGAACGAC 58.897 45.455 8.09 0.00 0.00 4.34
4321 4505 4.621991 AGAACACATACACACACTGACTC 58.378 43.478 0.00 0.00 0.00 3.36
4322 4506 4.501571 GGAGAACACATACACACACTGACT 60.502 45.833 0.00 0.00 0.00 3.41
4346 4530 1.452025 CTGTGTTACTGCAGTTCGTCG 59.548 52.381 27.06 6.03 0.00 5.12
4355 4539 3.005472 TCCTAGTGTCACTGTGTTACTGC 59.995 47.826 16.03 7.75 0.00 4.40
4362 4546 1.821753 CTCCCTCCTAGTGTCACTGTG 59.178 57.143 16.03 0.17 0.00 3.66
4368 4552 0.927767 TCCCTCTCCCTCCTAGTGTC 59.072 60.000 0.00 0.00 0.00 3.67
4373 4557 1.298693 TCTCTCTCCCTCTCCCTCCTA 59.701 57.143 0.00 0.00 0.00 2.94
4374 4558 0.047176 TCTCTCTCCCTCTCCCTCCT 59.953 60.000 0.00 0.00 0.00 3.69
4375 4559 0.478507 CTCTCTCTCCCTCTCCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
4376 4560 1.133792 CACTCTCTCTCCCTCTCCCTC 60.134 61.905 0.00 0.00 0.00 4.30
4377 4561 0.926293 CACTCTCTCTCCCTCTCCCT 59.074 60.000 0.00 0.00 0.00 4.20
4385 4572 3.686016 ACTGTTCTCTCACTCTCTCTCC 58.314 50.000 0.00 0.00 0.00 3.71
4386 4573 5.488341 ACTACTGTTCTCTCACTCTCTCTC 58.512 45.833 0.00 0.00 0.00 3.20
4395 4590 4.035612 ACCAGCTACTACTGTTCTCTCA 57.964 45.455 0.00 0.00 35.83 3.27


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

AutoCloner maintained by Alex Coulton.