Multiple sequence alignment - TraesCS6A01G311700

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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 TraesCS6A01G311700 chr6A 100.000 4343 0 0 860 5202 547821885 547826227 0.000000e+00 8021.0
1 TraesCS6A01G311700 chr6A 100.000 497 0 0 1 497 547821026 547821522 0.000000e+00 918.0
2 TraesCS6A01G311700 chr6D 92.571 2450 105 24 882 3305 401300868 401303266 0.000000e+00 3445.0
3 TraesCS6A01G311700 chr6D 93.698 603 29 6 3994 4589 401303776 401304376 0.000000e+00 894.0
4 TraesCS6A01G311700 chr6D 91.776 535 28 8 4677 5202 401305110 401305637 0.000000e+00 730.0
5 TraesCS6A01G311700 chr6D 89.498 438 10 5 1 425 401299906 401300320 5.970000e-144 521.0
6 TraesCS6A01G311700 chr6D 88.919 370 27 6 3495 3852 401303276 401303643 1.330000e-120 444.0
7 TraesCS6A01G311700 chr6D 93.578 109 5 2 3892 4000 401303647 401303753 1.500000e-35 161.0
8 TraesCS6A01G311700 chr6B 91.901 1704 82 24 876 2540 601873722 601875408 0.000000e+00 2331.0
9 TraesCS6A01G311700 chr6B 97.120 764 21 1 2543 3305 601875534 601876297 0.000000e+00 1288.0
10 TraesCS6A01G311700 chr6B 94.494 563 26 5 3994 4553 601876846 601877406 0.000000e+00 863.0
11 TraesCS6A01G311700 chr6B 88.084 621 53 13 4594 5202 601878869 601879480 0.000000e+00 717.0
12 TraesCS6A01G311700 chr6B 90.787 521 24 7 3497 4000 601876310 601876823 0.000000e+00 675.0
13 TraesCS6A01G311700 chr6B 83.752 597 60 17 951 1540 663290996 663291562 9.920000e-147 531.0
14 TraesCS6A01G311700 chr6B 92.308 169 10 3 259 425 601873333 601873500 2.420000e-58 237.0
15 TraesCS6A01G311700 chr5B 85.067 596 54 15 951 1540 28668364 28668930 4.520000e-160 575.0
16 TraesCS6A01G311700 chr7B 84.899 596 55 14 951 1540 579561517 579560951 2.100000e-158 569.0
17 TraesCS6A01G311700 chr7B 84.813 428 55 6 1962 2389 186745478 186745895 6.230000e-114 422.0
18 TraesCS6A01G311700 chr7B 80.068 296 36 18 1124 1413 118976137 118976415 1.140000e-46 198.0
19 TraesCS6A01G311700 chr1B 81.988 644 70 23 906 1540 177478201 177477595 6.010000e-139 505.0
20 TraesCS6A01G311700 chr7D 85.417 288 30 6 2105 2389 534870750 534870472 6.590000e-74 289.0
21 TraesCS6A01G311700 chr7D 92.593 135 10 0 1281 1415 156684568 156684702 1.480000e-45 195.0
22 TraesCS6A01G311700 chr7D 93.220 59 3 1 1124 1181 156684422 156684480 9.280000e-13 86.1
23 TraesCS6A01G311700 chr7D 77.551 98 17 4 2304 2400 285258833 285258740 3.000000e-03 54.7
24 TraesCS6A01G311700 chr7D 100.000 28 0 0 2304 2331 285258928 285258901 9.000000e-03 52.8
25 TraesCS6A01G311700 chr7A 93.333 135 9 0 1281 1415 211637940 211638074 3.180000e-47 200.0
26 TraesCS6A01G311700 chr7A 93.220 59 3 1 1124 1181 211637793 211637851 9.280000e-13 86.1


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 TraesCS6A01G311700 chr6A 547821026 547826227 5201 False 4469.5 8021 100.000000 1 5202 2 chr6A.!!$F1 5201
1 TraesCS6A01G311700 chr6D 401299906 401305637 5731 False 1032.5 3445 91.673333 1 5202 6 chr6D.!!$F1 5201
2 TraesCS6A01G311700 chr6B 601873333 601879480 6147 False 1018.5 2331 92.449000 259 5202 6 chr6B.!!$F2 4943
3 TraesCS6A01G311700 chr6B 663290996 663291562 566 False 531.0 531 83.752000 951 1540 1 chr6B.!!$F1 589
4 TraesCS6A01G311700 chr5B 28668364 28668930 566 False 575.0 575 85.067000 951 1540 1 chr5B.!!$F1 589
5 TraesCS6A01G311700 chr7B 579560951 579561517 566 True 569.0 569 84.899000 951 1540 1 chr7B.!!$R1 589
6 TraesCS6A01G311700 chr1B 177477595 177478201 606 True 505.0 505 81.988000 906 1540 1 chr1B.!!$R1 634

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
930 1079 0.251209 CCTCCTCCGATCCGATACCA 60.251 60.0 0.0 0.0 0.00 3.25 F
1223 1398 0.110509 CGTCCGTATGACCGTATCCG 60.111 60.0 0.0 0.0 41.18 4.18 F
2998 3346 0.388520 GTTGGACAAAGGGCGATTGC 60.389 55.0 0.0 0.0 41.71 3.56 F
3336 3685 0.034670 GCTGTTGCTCCCCTCATTCT 60.035 55.0 0.0 0.0 36.03 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2795 3116 0.538057 TTGGTTCCAGCTGGCTTCTG 60.538 55.0 28.91 3.15 34.44 3.02 R
3001 3349 0.106318 GGCAAGGCTCTCCCAATCAT 60.106 55.0 0.00 0.00 35.39 2.45 R
4099 4502 0.108804 ACTTCCACGCATCCACGTAG 60.109 55.0 0.00 0.00 46.34 3.51 R
4209 4612 0.676782 ACTACCGTGCTTGGGATTGC 60.677 55.0 0.00 0.00 0.00 3.56 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
38 39 0.436531 GTCGCGCTTTCTGAAGAGTG 59.563 55.000 5.56 8.04 42.34 3.51
40 41 1.630244 CGCGCTTTCTGAAGAGTGGG 61.630 60.000 5.56 12.13 38.86 4.61
146 147 3.524648 AACACGATTCCACCGCGGT 62.525 57.895 28.70 28.70 35.57 5.68
443 510 3.851128 GCCGCCCTCTCTACCCAC 61.851 72.222 0.00 0.00 0.00 4.61
496 567 1.732259 GAGCGCATCGGAAAGAGAAAA 59.268 47.619 11.47 0.00 0.00 2.29
899 1048 4.852138 TCTGTCTATAATAACACCGCGAC 58.148 43.478 8.23 0.00 0.00 5.19
900 1049 4.336153 TCTGTCTATAATAACACCGCGACA 59.664 41.667 8.23 0.00 0.00 4.35
901 1050 4.996344 TGTCTATAATAACACCGCGACAA 58.004 39.130 8.23 0.00 0.00 3.18
902 1051 5.593968 TGTCTATAATAACACCGCGACAAT 58.406 37.500 8.23 0.00 0.00 2.71
903 1052 6.044046 TGTCTATAATAACACCGCGACAATT 58.956 36.000 8.23 2.49 0.00 2.32
904 1053 6.019398 TGTCTATAATAACACCGCGACAATTG 60.019 38.462 8.23 3.24 0.00 2.32
930 1079 0.251209 CCTCCTCCGATCCGATACCA 60.251 60.000 0.00 0.00 0.00 3.25
1031 1180 4.821589 CCCCTCTTCGACAGCCGC 62.822 72.222 0.00 0.00 38.37 6.53
1214 1389 0.527113 TTTCCTTCGCGTCCGTATGA 59.473 50.000 5.77 0.00 35.54 2.15
1222 1397 0.386478 GCGTCCGTATGACCGTATCC 60.386 60.000 0.00 0.00 41.18 2.59
1223 1398 0.110509 CGTCCGTATGACCGTATCCG 60.111 60.000 0.00 0.00 41.18 4.18
1235 1411 4.201679 TATCCGTCCTGGCGCGTG 62.202 66.667 8.43 0.00 37.80 5.34
1258 1434 2.832129 AGAGATCTGCGTTTCCCTTACA 59.168 45.455 0.00 0.00 0.00 2.41
1444 1629 2.419851 CCTCTCATCCTTCTGCCTGTTC 60.420 54.545 0.00 0.00 0.00 3.18
1485 1678 7.234782 TCGTAGTATATCTTCATTCATGGGGTT 59.765 37.037 0.00 0.00 0.00 4.11
1490 1683 4.656100 TCTTCATTCATGGGGTTCTGAA 57.344 40.909 0.00 0.00 35.95 3.02
1500 1693 3.157087 TGGGGTTCTGAATTCTGCTTTC 58.843 45.455 7.05 0.00 0.00 2.62
1514 1710 3.010472 TCTGCTTTCAATCAATCCCCTGA 59.990 43.478 0.00 0.00 0.00 3.86
1526 1722 3.825908 ATCCCCTGAGAGTAGATCCTC 57.174 52.381 0.00 0.00 0.00 3.71
1610 1806 3.152341 AGAACTCAAGGTTTGCATCTGG 58.848 45.455 0.00 0.00 38.41 3.86
1619 1816 2.299867 GGTTTGCATCTGGTTTCCATGT 59.700 45.455 0.00 0.00 30.82 3.21
1624 1821 3.018856 GCATCTGGTTTCCATGTGATCA 58.981 45.455 0.00 0.00 30.82 2.92
1634 1831 2.158914 TCCATGTGATCATTCCACCGAG 60.159 50.000 0.00 0.00 33.80 4.63
1637 1834 3.694043 TGTGATCATTCCACCGAGAAA 57.306 42.857 0.00 0.00 33.80 2.52
1769 1966 2.424601 TCTGCTGCCAATGTATGCTTTC 59.575 45.455 0.00 0.00 0.00 2.62
1809 2006 2.371841 TGCATCTATCCATGTGGTACCC 59.628 50.000 10.07 1.05 36.34 3.69
1870 2067 8.299570 GTTCCATTTGATGTTGTAAAGATGTCT 58.700 33.333 0.00 0.00 25.38 3.41
2007 2205 3.262915 AGATCTGGTATGGCTGCTTATCC 59.737 47.826 0.00 0.00 0.00 2.59
2015 2213 1.202533 TGGCTGCTTATCCGCTCTAAC 60.203 52.381 0.00 0.00 0.00 2.34
2062 2260 1.039856 ATTTTGTCGTGCCAGGCTTT 58.960 45.000 14.15 0.00 0.00 3.51
2081 2279 5.050159 GGCTTTGAATTTTGGTTGTCACATC 60.050 40.000 0.00 0.00 0.00 3.06
2145 2343 6.405538 TCAAAATTTTGTGAAGCTGTTCCTT 58.594 32.000 25.98 0.00 39.18 3.36
2190 2388 6.347696 TGCATTTCCTTGTTTCTGTTTTGAT 58.652 32.000 0.00 0.00 0.00 2.57
2241 2439 7.369607 TGTTGTTGATTGGTATGAAATCTGTG 58.630 34.615 0.00 0.00 35.48 3.66
2354 2552 3.976793 TGTACTATTTCCTCGGCGTAG 57.023 47.619 6.85 2.31 0.00 3.51
2368 2566 2.260481 GGCGTAGTTCTTCAGCTGTAC 58.740 52.381 14.67 6.72 0.00 2.90
2386 2584 7.815068 CAGCTGTACTAGTATGAATACCAATCC 59.185 40.741 5.25 0.00 33.79 3.01
2493 2691 4.194640 TGAAGCTCATTGAGAAGGTATGC 58.805 43.478 17.87 0.05 0.00 3.14
2517 2798 7.701924 TGCATGCTGTTACAAAATAAATAGCTC 59.298 33.333 20.33 0.00 39.66 4.09
2602 2923 9.533253 AATGTTATTTGCACCTAAATGATAAGC 57.467 29.630 0.00 0.00 32.79 3.09
2605 2926 5.888691 TTTGCACCTAAATGATAAGCGAA 57.111 34.783 0.00 0.00 0.00 4.70
2623 2944 3.369451 GCGAAGTTCCTGAATCTGTTCTC 59.631 47.826 0.00 0.00 35.33 2.87
2795 3116 9.216117 ACTGAACTCACTAACATTGGTATAAAC 57.784 33.333 0.00 0.00 0.00 2.01
2818 3139 1.109323 AGCCAGCTGGAACCAACAAC 61.109 55.000 37.21 14.89 37.39 3.32
2979 3327 5.699915 CAGGAGCCTGATGACTGTAATAATG 59.300 44.000 11.08 0.00 46.30 1.90
2980 3328 5.367937 AGGAGCCTGATGACTGTAATAATGT 59.632 40.000 0.00 0.00 0.00 2.71
2981 3329 6.058183 GGAGCCTGATGACTGTAATAATGTT 58.942 40.000 0.00 0.00 0.00 2.71
2982 3330 6.017605 GGAGCCTGATGACTGTAATAATGTTG 60.018 42.308 0.00 0.00 0.00 3.33
2983 3331 5.824624 AGCCTGATGACTGTAATAATGTTGG 59.175 40.000 0.00 0.00 0.00 3.77
2984 3332 5.822519 GCCTGATGACTGTAATAATGTTGGA 59.177 40.000 0.00 0.00 0.00 3.53
2985 3333 6.238484 GCCTGATGACTGTAATAATGTTGGAC 60.238 42.308 0.00 0.00 0.00 4.02
2986 3334 6.823182 CCTGATGACTGTAATAATGTTGGACA 59.177 38.462 0.00 0.00 0.00 4.02
2987 3335 7.336679 CCTGATGACTGTAATAATGTTGGACAA 59.663 37.037 0.00 0.00 0.00 3.18
2988 3336 8.628630 TGATGACTGTAATAATGTTGGACAAA 57.371 30.769 0.00 0.00 0.00 2.83
2989 3337 8.729756 TGATGACTGTAATAATGTTGGACAAAG 58.270 33.333 0.00 0.00 0.00 2.77
2990 3338 7.447374 TGACTGTAATAATGTTGGACAAAGG 57.553 36.000 0.00 0.00 0.00 3.11
2991 3339 6.432783 TGACTGTAATAATGTTGGACAAAGGG 59.567 38.462 0.00 0.00 0.00 3.95
2992 3340 5.185056 ACTGTAATAATGTTGGACAAAGGGC 59.815 40.000 0.00 0.00 0.00 5.19
2993 3341 3.866883 AATAATGTTGGACAAAGGGCG 57.133 42.857 0.00 0.00 0.00 6.13
2994 3342 2.570415 TAATGTTGGACAAAGGGCGA 57.430 45.000 0.00 0.00 0.00 5.54
2995 3343 1.923356 AATGTTGGACAAAGGGCGAT 58.077 45.000 0.00 0.00 0.00 4.58
2996 3344 1.923356 ATGTTGGACAAAGGGCGATT 58.077 45.000 0.00 0.00 0.00 3.34
2997 3345 0.958091 TGTTGGACAAAGGGCGATTG 59.042 50.000 0.00 0.01 0.00 2.67
2998 3346 0.388520 GTTGGACAAAGGGCGATTGC 60.389 55.000 0.00 0.00 41.71 3.56
3305 3654 6.135290 TGCTTCTTATTTGTCATGCATACC 57.865 37.500 0.00 0.00 0.00 2.73
3306 3655 5.651576 TGCTTCTTATTTGTCATGCATACCA 59.348 36.000 0.00 0.00 0.00 3.25
3307 3656 6.152492 TGCTTCTTATTTGTCATGCATACCAA 59.848 34.615 0.00 2.20 0.00 3.67
3308 3657 6.473455 GCTTCTTATTTGTCATGCATACCAAC 59.527 38.462 0.00 0.00 0.00 3.77
3309 3658 7.629222 GCTTCTTATTTGTCATGCATACCAACT 60.629 37.037 0.00 2.43 0.00 3.16
3312 3661 7.557358 TCTTATTTGTCATGCATACCAACTGAT 59.443 33.333 0.00 0.00 0.00 2.90
3313 3662 8.744568 TTATTTGTCATGCATACCAACTGATA 57.255 30.769 0.00 0.00 0.00 2.15
3314 3663 7.828508 ATTTGTCATGCATACCAACTGATAT 57.171 32.000 0.00 0.00 0.00 1.63
3315 3664 6.866010 TTGTCATGCATACCAACTGATATC 57.134 37.500 0.00 0.00 0.00 1.63
3316 3665 6.178607 TGTCATGCATACCAACTGATATCT 57.821 37.500 0.00 0.00 0.00 1.98
3317 3666 5.993441 TGTCATGCATACCAACTGATATCTG 59.007 40.000 0.00 7.98 0.00 2.90
3318 3667 4.999311 TCATGCATACCAACTGATATCTGC 59.001 41.667 0.00 6.03 0.00 4.26
3319 3668 4.694760 TGCATACCAACTGATATCTGCT 57.305 40.909 9.35 0.00 0.00 4.24
3320 3669 4.383173 TGCATACCAACTGATATCTGCTG 58.617 43.478 9.35 7.63 0.00 4.41
3321 3670 4.141642 TGCATACCAACTGATATCTGCTGT 60.142 41.667 9.35 6.92 0.00 4.40
3322 3671 4.818546 GCATACCAACTGATATCTGCTGTT 59.181 41.667 9.35 0.00 0.00 3.16
3323 3672 5.277683 GCATACCAACTGATATCTGCTGTTG 60.278 44.000 9.35 13.97 41.75 3.33
3324 3673 3.012518 ACCAACTGATATCTGCTGTTGC 58.987 45.455 17.58 0.00 41.17 4.17
3325 3674 3.276857 CCAACTGATATCTGCTGTTGCT 58.723 45.455 17.58 0.00 41.17 3.91
3326 3675 3.311871 CCAACTGATATCTGCTGTTGCTC 59.688 47.826 17.58 0.00 41.17 4.26
3327 3676 3.191078 ACTGATATCTGCTGTTGCTCC 57.809 47.619 9.35 0.00 40.48 4.70
3328 3677 2.158842 ACTGATATCTGCTGTTGCTCCC 60.159 50.000 9.35 0.00 40.48 4.30
3329 3678 1.141657 TGATATCTGCTGTTGCTCCCC 59.858 52.381 3.98 0.00 40.48 4.81
3330 3679 1.419387 GATATCTGCTGTTGCTCCCCT 59.581 52.381 0.00 0.00 40.48 4.79
3331 3680 0.833287 TATCTGCTGTTGCTCCCCTC 59.167 55.000 0.00 0.00 40.48 4.30
3332 3681 1.203441 ATCTGCTGTTGCTCCCCTCA 61.203 55.000 0.00 0.00 40.48 3.86
3333 3682 1.203441 TCTGCTGTTGCTCCCCTCAT 61.203 55.000 0.00 0.00 40.48 2.90
3334 3683 0.323178 CTGCTGTTGCTCCCCTCATT 60.323 55.000 0.00 0.00 40.48 2.57
3335 3684 0.322816 TGCTGTTGCTCCCCTCATTC 60.323 55.000 0.00 0.00 40.48 2.67
3336 3685 0.034670 GCTGTTGCTCCCCTCATTCT 60.035 55.000 0.00 0.00 36.03 2.40
3337 3686 2.016096 GCTGTTGCTCCCCTCATTCTC 61.016 57.143 0.00 0.00 36.03 2.87
3338 3687 1.558756 CTGTTGCTCCCCTCATTCTCT 59.441 52.381 0.00 0.00 0.00 3.10
3339 3688 1.988107 TGTTGCTCCCCTCATTCTCTT 59.012 47.619 0.00 0.00 0.00 2.85
3340 3689 2.376518 TGTTGCTCCCCTCATTCTCTTT 59.623 45.455 0.00 0.00 0.00 2.52
3341 3690 3.181429 TGTTGCTCCCCTCATTCTCTTTT 60.181 43.478 0.00 0.00 0.00 2.27
3342 3691 3.814504 TGCTCCCCTCATTCTCTTTTT 57.185 42.857 0.00 0.00 0.00 1.94
3371 3720 9.557061 CTCCCCTTGTATTCTTAACTATAAACC 57.443 37.037 0.00 0.00 0.00 3.27
3372 3721 8.206189 TCCCCTTGTATTCTTAACTATAAACCG 58.794 37.037 0.00 0.00 0.00 4.44
3373 3722 8.206189 CCCCTTGTATTCTTAACTATAAACCGA 58.794 37.037 0.00 0.00 0.00 4.69
3374 3723 9.603921 CCCTTGTATTCTTAACTATAAACCGAA 57.396 33.333 0.00 0.00 0.00 4.30
3381 3730 8.752766 TTCTTAACTATAAACCGAAGAGTGTG 57.247 34.615 0.00 0.00 0.00 3.82
3382 3731 7.318141 TCTTAACTATAAACCGAAGAGTGTGG 58.682 38.462 0.00 0.00 0.00 4.17
3383 3732 5.733620 AACTATAAACCGAAGAGTGTGGA 57.266 39.130 0.00 0.00 0.00 4.02
3384 3733 5.733620 ACTATAAACCGAAGAGTGTGGAA 57.266 39.130 0.00 0.00 0.00 3.53
3385 3734 6.105397 ACTATAAACCGAAGAGTGTGGAAA 57.895 37.500 0.00 0.00 0.00 3.13
3386 3735 5.930569 ACTATAAACCGAAGAGTGTGGAAAC 59.069 40.000 0.00 0.00 0.00 2.78
3387 3736 3.277142 AAACCGAAGAGTGTGGAAACT 57.723 42.857 0.00 0.00 0.00 2.66
3388 3737 3.277142 AACCGAAGAGTGTGGAAACTT 57.723 42.857 0.00 0.00 0.00 2.66
3389 3738 3.277142 ACCGAAGAGTGTGGAAACTTT 57.723 42.857 0.00 0.00 0.00 2.66
3390 3739 3.617284 ACCGAAGAGTGTGGAAACTTTT 58.383 40.909 0.00 0.00 0.00 2.27
3391 3740 4.014406 ACCGAAGAGTGTGGAAACTTTTT 58.986 39.130 0.00 0.00 0.00 1.94
3392 3741 4.142469 ACCGAAGAGTGTGGAAACTTTTTG 60.142 41.667 0.00 0.00 0.00 2.44
3393 3742 3.791353 CGAAGAGTGTGGAAACTTTTTGC 59.209 43.478 0.00 0.00 0.00 3.68
3394 3743 4.438744 CGAAGAGTGTGGAAACTTTTTGCT 60.439 41.667 0.00 0.00 0.00 3.91
3395 3744 5.405935 AAGAGTGTGGAAACTTTTTGCTT 57.594 34.783 0.00 0.00 0.00 3.91
3396 3745 4.998788 AGAGTGTGGAAACTTTTTGCTTC 58.001 39.130 0.00 0.00 0.00 3.86
3397 3746 4.112634 GAGTGTGGAAACTTTTTGCTTCC 58.887 43.478 0.00 0.00 40.41 3.46
3398 3747 3.513515 AGTGTGGAAACTTTTTGCTTCCA 59.486 39.130 0.00 0.00 45.56 3.53
3401 3750 4.543590 TGGAAACTTTTTGCTTCCAACA 57.456 36.364 0.32 0.00 45.00 3.33
3402 3751 4.899502 TGGAAACTTTTTGCTTCCAACAA 58.100 34.783 0.32 0.00 45.00 2.83
3403 3752 4.693095 TGGAAACTTTTTGCTTCCAACAAC 59.307 37.500 0.32 0.00 45.00 3.32
3404 3753 4.094294 GGAAACTTTTTGCTTCCAACAACC 59.906 41.667 0.00 0.00 39.91 3.77
3405 3754 3.260475 ACTTTTTGCTTCCAACAACCC 57.740 42.857 0.00 0.00 0.00 4.11
3406 3755 2.093181 ACTTTTTGCTTCCAACAACCCC 60.093 45.455 0.00 0.00 0.00 4.95
3407 3756 1.573108 TTTTGCTTCCAACAACCCCA 58.427 45.000 0.00 0.00 0.00 4.96
3408 3757 1.799933 TTTGCTTCCAACAACCCCAT 58.200 45.000 0.00 0.00 0.00 4.00
3409 3758 1.047002 TTGCTTCCAACAACCCCATG 58.953 50.000 0.00 0.00 0.00 3.66
3410 3759 0.105760 TGCTTCCAACAACCCCATGT 60.106 50.000 0.00 0.00 34.24 3.21
3411 3760 1.145945 TGCTTCCAACAACCCCATGTA 59.854 47.619 0.00 0.00 32.02 2.29
3412 3761 2.243810 GCTTCCAACAACCCCATGTAA 58.756 47.619 0.00 0.00 32.02 2.41
3413 3762 2.831526 GCTTCCAACAACCCCATGTAAT 59.168 45.455 0.00 0.00 32.02 1.89
3414 3763 3.260632 GCTTCCAACAACCCCATGTAATT 59.739 43.478 0.00 0.00 32.02 1.40
3415 3764 4.262851 GCTTCCAACAACCCCATGTAATTT 60.263 41.667 0.00 0.00 32.02 1.82
3416 3765 4.881019 TCCAACAACCCCATGTAATTTG 57.119 40.909 0.00 0.00 32.02 2.32
3417 3766 4.483950 TCCAACAACCCCATGTAATTTGA 58.516 39.130 0.00 0.00 32.02 2.69
3418 3767 4.282195 TCCAACAACCCCATGTAATTTGAC 59.718 41.667 0.00 0.00 32.02 3.18
3419 3768 4.562552 CCAACAACCCCATGTAATTTGACC 60.563 45.833 0.00 0.00 32.02 4.02
3420 3769 4.126520 ACAACCCCATGTAATTTGACCT 57.873 40.909 0.00 0.00 0.00 3.85
3421 3770 4.086457 ACAACCCCATGTAATTTGACCTC 58.914 43.478 0.00 0.00 0.00 3.85
3422 3771 4.202673 ACAACCCCATGTAATTTGACCTCT 60.203 41.667 0.00 0.00 0.00 3.69
3423 3772 3.968265 ACCCCATGTAATTTGACCTCTG 58.032 45.455 0.00 0.00 0.00 3.35
3424 3773 3.290710 CCCCATGTAATTTGACCTCTGG 58.709 50.000 0.00 0.00 0.00 3.86
3425 3774 3.309121 CCCCATGTAATTTGACCTCTGGT 60.309 47.826 0.00 0.00 39.44 4.00
3434 3783 3.083997 ACCTCTGGTCATCCGGGC 61.084 66.667 0.00 0.00 40.36 6.13
3435 3784 2.765807 CCTCTGGTCATCCGGGCT 60.766 66.667 0.00 0.00 40.36 5.19
3436 3785 1.457643 CCTCTGGTCATCCGGGCTA 60.458 63.158 0.00 0.00 40.36 3.93
3437 3786 1.742768 CTCTGGTCATCCGGGCTAC 59.257 63.158 0.00 0.00 40.36 3.58
3438 3787 2.076622 CTCTGGTCATCCGGGCTACG 62.077 65.000 0.00 0.00 40.36 3.51
3447 3796 3.663202 CGGGCTACGGCTTGTTTT 58.337 55.556 0.00 0.00 39.42 2.43
3448 3797 1.209127 CGGGCTACGGCTTGTTTTG 59.791 57.895 0.00 0.00 39.42 2.44
3449 3798 1.231958 CGGGCTACGGCTTGTTTTGA 61.232 55.000 0.00 0.00 39.42 2.69
3450 3799 0.955905 GGGCTACGGCTTGTTTTGAA 59.044 50.000 0.00 0.00 38.73 2.69
3451 3800 1.544246 GGGCTACGGCTTGTTTTGAAT 59.456 47.619 0.00 0.00 38.73 2.57
3452 3801 2.595386 GGCTACGGCTTGTTTTGAATG 58.405 47.619 0.00 0.00 38.73 2.67
3453 3802 1.985684 GCTACGGCTTGTTTTGAATGC 59.014 47.619 0.00 0.00 35.22 3.56
3454 3803 2.606795 GCTACGGCTTGTTTTGAATGCA 60.607 45.455 0.00 0.00 35.22 3.96
3455 3804 2.818130 ACGGCTTGTTTTGAATGCAT 57.182 40.000 0.00 0.00 0.00 3.96
3456 3805 2.406130 ACGGCTTGTTTTGAATGCATG 58.594 42.857 0.00 0.00 0.00 4.06
3457 3806 2.035704 ACGGCTTGTTTTGAATGCATGA 59.964 40.909 0.00 0.00 0.00 3.07
3458 3807 2.664568 CGGCTTGTTTTGAATGCATGAG 59.335 45.455 0.00 0.00 0.00 2.90
3459 3808 2.997986 GGCTTGTTTTGAATGCATGAGG 59.002 45.455 0.00 0.00 0.00 3.86
3460 3809 2.414138 GCTTGTTTTGAATGCATGAGGC 59.586 45.455 0.00 0.00 45.13 4.70
3472 3821 3.137446 GCATGAGGCAGATAATGGTCT 57.863 47.619 0.00 0.00 43.97 3.85
3473 3822 2.812591 GCATGAGGCAGATAATGGTCTG 59.187 50.000 0.00 3.79 46.59 3.51
3483 3832 6.521151 CAGATAATGGTCTGCCTTTTTCTT 57.479 37.500 0.00 0.00 37.77 2.52
3484 3833 6.928520 CAGATAATGGTCTGCCTTTTTCTTT 58.071 36.000 0.00 0.00 37.77 2.52
3485 3834 7.031975 CAGATAATGGTCTGCCTTTTTCTTTC 58.968 38.462 0.00 0.00 37.77 2.62
3486 3835 6.721208 AGATAATGGTCTGCCTTTTTCTTTCA 59.279 34.615 0.00 0.00 37.10 2.69
3487 3836 5.612725 AATGGTCTGCCTTTTTCTTTCAA 57.387 34.783 0.00 0.00 35.27 2.69
3488 3837 5.612725 ATGGTCTGCCTTTTTCTTTCAAA 57.387 34.783 0.00 0.00 35.27 2.69
3489 3838 5.413309 TGGTCTGCCTTTTTCTTTCAAAA 57.587 34.783 0.00 0.00 35.27 2.44
3490 3839 5.799213 TGGTCTGCCTTTTTCTTTCAAAAA 58.201 33.333 0.00 0.00 35.27 1.94
3551 3901 6.323482 TCAGAATCAACCTTCCAAATGAAACA 59.677 34.615 0.00 0.00 31.06 2.83
3705 4071 3.259876 TCGGTCTATGCAAGTGGTAGTTT 59.740 43.478 0.00 0.00 0.00 2.66
3737 4103 1.002430 TCCAGTGCGAAAGAAGATGCT 59.998 47.619 0.00 0.00 0.00 3.79
3759 4125 7.949434 TGCTCATAGCTCCATACATATATGAG 58.051 38.462 19.63 13.20 44.73 2.90
3867 4236 5.342806 TGTTTTTCACAATGAGCTACTCG 57.657 39.130 0.00 0.00 29.53 4.18
3949 4318 5.069648 CCATCAATTACAGAGCTCTGACCTA 59.930 44.000 42.76 25.58 46.59 3.08
3962 4331 8.543774 AGAGCTCTGACCTATTTTGAGAATTTA 58.456 33.333 17.42 0.00 0.00 1.40
4042 4439 8.533569 AATCTTCCCCGTTATAATGTCAAAAT 57.466 30.769 4.04 0.00 0.00 1.82
4060 4457 5.009210 TCAAAATACTGACAGTTTTTCCCCG 59.991 40.000 19.97 11.62 30.07 5.73
4090 4493 2.433318 GCAGCACTCGGTGACCTC 60.433 66.667 0.00 0.00 43.56 3.85
4099 4502 0.033504 TCGGTGACCTCTTTGCTCAC 59.966 55.000 0.00 0.00 34.68 3.51
4209 4612 7.867445 ATAAACGATTTTTGTAGGCAAACTG 57.133 32.000 0.00 0.00 43.47 3.16
4223 4626 0.314935 AAACTGCAATCCCAAGCACG 59.685 50.000 0.00 0.00 36.62 5.34
4338 4742 7.988737 TGTATTTACTCAATGCAGGAAATCTG 58.011 34.615 6.28 0.00 46.03 2.90
4347 4751 3.347216 TGCAGGAAATCTGTAGGCTTTC 58.653 45.455 0.00 0.00 45.08 2.62
4394 4798 7.283127 ACATTTTCTCACTGTCAATGTGTAACT 59.717 33.333 0.00 0.00 36.84 2.24
4445 4849 1.065926 TGTGCCTACCTCTGCATTCTG 60.066 52.381 0.00 0.00 40.07 3.02
4453 4857 2.015587 CCTCTGCATTCTGAAGCTTCC 58.984 52.381 23.42 7.55 0.00 3.46
4465 4869 0.878416 AAGCTTCCGTTTTGCGCATA 59.122 45.000 12.75 2.60 39.71 3.14
4472 4876 2.744741 TCCGTTTTGCGCATATCTTTCA 59.255 40.909 12.75 0.00 39.71 2.69
4514 4919 2.386661 ACACTATTGTTCGCCAGAGG 57.613 50.000 0.00 0.00 28.43 3.69
4590 6382 3.608316 TGAAAGCAAGGCAAAACACTT 57.392 38.095 0.00 0.00 0.00 3.16
4619 6447 5.237048 GCTGGTATTTTTCCAATTCAAGCA 58.763 37.500 0.00 0.00 34.35 3.91
4630 6458 7.994425 TTCCAATTCAAGCAGACTATTACAA 57.006 32.000 0.00 0.00 0.00 2.41
4675 6503 4.274459 GGTGCTAGGAAGTTTGCATATGAG 59.726 45.833 6.97 0.00 37.76 2.90
4678 7116 5.355071 TGCTAGGAAGTTTGCATATGAGTTG 59.645 40.000 6.97 0.00 0.00 3.16
4700 7138 3.004419 GCTAGAAACCTTCGCCTGTTTTT 59.996 43.478 0.00 0.00 34.97 1.94
4706 7144 1.602920 CCTTCGCCTGTTTTTGCCTTC 60.603 52.381 0.00 0.00 0.00 3.46
4739 7177 5.129320 ACCCTGCACTTTTTCTTCTTTTGAT 59.871 36.000 0.00 0.00 0.00 2.57
4755 7193 1.737838 TGATACCAAAGAAGCCTGCG 58.262 50.000 0.00 0.00 0.00 5.18
4774 7212 2.281498 GCGCTTGTTTTCACCTGTTTTC 59.719 45.455 0.00 0.00 0.00 2.29
4778 7217 5.802956 CGCTTGTTTTCACCTGTTTTCTTTA 59.197 36.000 0.00 0.00 0.00 1.85
4907 7355 1.688197 CATTGCCAGGGTTGTTTCACT 59.312 47.619 0.00 0.00 0.00 3.41
4929 7377 8.733458 TCACTTTGTTTATGATGAAAGAGGATG 58.267 33.333 0.00 0.00 31.24 3.51
4931 7379 7.671398 ACTTTGTTTATGATGAAAGAGGATGGT 59.329 33.333 0.00 0.00 31.24 3.55
4933 7381 7.395190 TGTTTATGATGAAAGAGGATGGTTG 57.605 36.000 0.00 0.00 0.00 3.77
4935 7383 4.598036 ATGATGAAAGAGGATGGTTGGT 57.402 40.909 0.00 0.00 0.00 3.67
5121 7570 4.267690 TGAAAATTGCGATGCTAGTCGTAG 59.732 41.667 4.86 0.00 43.27 3.51
5144 7593 9.608617 GTAGCATCAATCATTAACATCATGAAG 57.391 33.333 0.00 0.00 34.31 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.250040 AGAAAGCGCGACAATGTAACTTT 59.750 39.130 12.10 6.25 0.00 2.66
38 39 0.323360 TGTGCCATGGCTTACTTCCC 60.323 55.000 35.53 14.04 42.51 3.97
40 41 0.447801 CGTGTGCCATGGCTTACTTC 59.552 55.000 35.53 20.70 42.51 3.01
162 163 2.709475 GAATCACGCGATGGCACC 59.291 61.111 15.93 0.00 39.92 5.01
163 164 2.709475 GGAATCACGCGATGGCAC 59.291 61.111 15.93 0.00 39.92 5.01
164 165 2.889988 CGGAATCACGCGATGGCA 60.890 61.111 15.93 0.00 39.92 4.92
473 540 4.271170 CTTTCCGATGCGCTCGCG 62.271 66.667 19.41 14.72 46.25 5.87
870 941 8.459635 GCGGTGTTATTATAGACAGATATGAGA 58.540 37.037 0.00 0.00 0.00 3.27
871 942 7.429630 CGCGGTGTTATTATAGACAGATATGAG 59.570 40.741 0.00 0.00 0.00 2.90
872 943 7.120138 TCGCGGTGTTATTATAGACAGATATGA 59.880 37.037 6.13 0.00 0.00 2.15
873 944 7.218393 GTCGCGGTGTTATTATAGACAGATATG 59.782 40.741 6.13 0.00 0.00 1.78
874 945 7.094506 TGTCGCGGTGTTATTATAGACAGATAT 60.095 37.037 6.13 0.00 34.01 1.63
879 950 4.635833 TGTCGCGGTGTTATTATAGACA 57.364 40.909 6.13 0.00 35.38 3.41
892 1041 0.109319 GGAATTGCAATTGTCGCGGT 60.109 50.000 28.67 2.19 0.00 5.68
899 1048 1.406539 CGGAGGAGGGAATTGCAATTG 59.593 52.381 28.67 7.61 0.00 2.32
900 1049 1.284785 TCGGAGGAGGGAATTGCAATT 59.715 47.619 24.33 24.33 0.00 2.32
901 1050 0.918983 TCGGAGGAGGGAATTGCAAT 59.081 50.000 5.99 5.99 0.00 3.56
902 1051 0.918983 ATCGGAGGAGGGAATTGCAA 59.081 50.000 0.00 0.00 0.00 4.08
903 1052 0.469917 GATCGGAGGAGGGAATTGCA 59.530 55.000 0.00 0.00 0.00 4.08
904 1053 0.250510 GGATCGGAGGAGGGAATTGC 60.251 60.000 0.00 0.00 0.00 3.56
947 1096 3.558411 GCAGGATCTGTGTCGCGC 61.558 66.667 0.00 0.00 33.43 6.86
1223 1398 4.803426 CTCTCCACGCGCCAGGAC 62.803 72.222 5.73 0.00 0.00 3.85
1235 1411 0.827368 AGGGAAACGCAGATCTCTCC 59.173 55.000 0.00 0.00 0.00 3.71
1236 1412 2.682155 AAGGGAAACGCAGATCTCTC 57.318 50.000 0.00 0.00 28.65 3.20
1237 1413 2.832129 TGTAAGGGAAACGCAGATCTCT 59.168 45.455 0.00 0.00 29.90 3.10
1258 1434 2.853210 CACGCGCACGAGAATTGT 59.147 55.556 5.73 0.00 43.93 2.71
1444 1629 3.212685 ACTACGAAGAAGTCTATCCGGG 58.787 50.000 0.00 0.00 0.00 5.73
1485 1678 6.127535 GGGATTGATTGAAAGCAGAATTCAGA 60.128 38.462 8.44 0.00 38.01 3.27
1490 1683 4.404715 CAGGGGATTGATTGAAAGCAGAAT 59.595 41.667 0.00 0.00 0.00 2.40
1500 1693 5.279910 GGATCTACTCTCAGGGGATTGATTG 60.280 48.000 0.00 0.00 0.00 2.67
1526 1722 2.047274 TTCTTGGCCTTCCTCGCG 60.047 61.111 3.32 0.00 0.00 5.87
1592 1788 2.664402 ACCAGATGCAAACCTTGAGT 57.336 45.000 0.00 0.00 0.00 3.41
1610 1806 3.181497 CGGTGGAATGATCACATGGAAAC 60.181 47.826 0.00 0.00 36.79 2.78
1619 1816 4.191544 GACATTTCTCGGTGGAATGATCA 58.808 43.478 15.92 0.00 0.00 2.92
1624 1821 3.338249 CACTGACATTTCTCGGTGGAAT 58.662 45.455 0.88 0.00 41.94 3.01
1634 1831 5.181009 TGAGATGGATCACACTGACATTTC 58.819 41.667 0.00 0.00 0.00 2.17
1637 1834 4.831674 TTGAGATGGATCACACTGACAT 57.168 40.909 0.00 0.00 0.00 3.06
1702 1899 1.899142 AGGCCAGACTTCTCTCTCAAC 59.101 52.381 5.01 0.00 0.00 3.18
1769 1966 3.005050 TGCAAAGGAAAGATGCAGACAAG 59.995 43.478 0.00 0.00 44.52 3.16
1809 2006 4.307432 AGTCAGGAACTACATTGTTCACG 58.693 43.478 9.18 0.00 45.74 4.35
1870 2067 4.036852 AGCTTATCATCGTCTTCGTCATCA 59.963 41.667 0.00 0.00 38.33 3.07
1914 2111 3.077556 TCAGCTTCTCGCCCTCCC 61.078 66.667 0.00 0.00 40.39 4.30
1984 2181 2.926778 AAGCAGCCATACCAGATCTC 57.073 50.000 0.00 0.00 0.00 2.75
2007 2205 3.084579 CAAGCCAGCGTTAGAGCG 58.915 61.111 0.00 0.00 43.00 5.03
2015 2213 1.308069 AACCATACAGCAAGCCAGCG 61.308 55.000 0.00 0.00 40.15 5.18
2062 2260 6.320926 TCTGAAGATGTGACAACCAAAATTCA 59.679 34.615 0.00 0.00 0.00 2.57
2081 2279 6.550854 AGACTTCTCCTTCCTATGATCTGAAG 59.449 42.308 0.00 0.00 36.19 3.02
2161 2359 5.776744 ACAGAAACAAGGAAATGCAGAATC 58.223 37.500 0.00 0.00 0.00 2.52
2190 2388 7.451255 AGTTCCACAAACCATAAATCTTCATCA 59.549 33.333 0.00 0.00 38.76 3.07
2241 2439 1.709147 CGTGCTAACCTGCTGGATGC 61.709 60.000 17.64 15.98 43.25 3.91
2354 2552 9.453325 GTATTCATACTAGTACAGCTGAAGAAC 57.547 37.037 23.35 12.44 34.49 3.01
2493 2691 9.740239 ATGAGCTATTTATTTTGTAACAGCATG 57.260 29.630 0.00 0.00 46.00 4.06
2517 2798 4.436332 TGAGTGCAGCTGACATACTTATG 58.564 43.478 20.43 0.00 39.55 1.90
2555 2876 4.908601 TTTTAAGACCATGCAGGAGAGA 57.091 40.909 0.00 0.00 41.22 3.10
2602 2923 3.610242 CGAGAACAGATTCAGGAACTTCG 59.390 47.826 0.00 0.00 34.60 3.79
2605 2926 4.873746 TTCGAGAACAGATTCAGGAACT 57.126 40.909 0.00 0.00 43.88 3.01
2623 2944 2.220824 TGTGTCTGCGTGAAAAGATTCG 59.779 45.455 0.00 0.00 38.46 3.34
2687 3008 4.444733 CCATTTTCTGCTTTTGGTTTCCCT 60.445 41.667 0.00 0.00 0.00 4.20
2795 3116 0.538057 TTGGTTCCAGCTGGCTTCTG 60.538 55.000 28.91 3.15 34.44 3.02
2818 3139 0.801251 CAGCTTCGCTTTCTTCTGGG 59.199 55.000 0.00 0.00 36.40 4.45
2979 3327 0.388520 GCAATCGCCCTTTGTCCAAC 60.389 55.000 0.00 0.00 0.00 3.77
2980 3328 1.963679 GCAATCGCCCTTTGTCCAA 59.036 52.632 0.00 0.00 0.00 3.53
2981 3329 3.680156 GCAATCGCCCTTTGTCCA 58.320 55.556 0.00 0.00 0.00 4.02
3000 3348 1.030457 GCAAGGCTCTCCCAATCATG 58.970 55.000 0.00 0.00 35.39 3.07
3001 3349 0.106318 GGCAAGGCTCTCCCAATCAT 60.106 55.000 0.00 0.00 35.39 2.45
3002 3350 1.304282 GGCAAGGCTCTCCCAATCA 59.696 57.895 0.00 0.00 35.39 2.57
3003 3351 1.821332 CGGCAAGGCTCTCCCAATC 60.821 63.158 0.00 0.00 35.39 2.67
3004 3352 1.639635 ATCGGCAAGGCTCTCCCAAT 61.640 55.000 0.00 0.00 35.39 3.16
3005 3353 1.852157 AATCGGCAAGGCTCTCCCAA 61.852 55.000 0.00 0.00 35.39 4.12
3305 3654 3.311871 GGAGCAACAGCAGATATCAGTTG 59.688 47.826 18.22 18.22 41.71 3.16
3306 3655 3.539604 GGAGCAACAGCAGATATCAGTT 58.460 45.455 5.32 1.67 0.00 3.16
3307 3656 2.158842 GGGAGCAACAGCAGATATCAGT 60.159 50.000 5.32 0.00 0.00 3.41
3308 3657 2.492012 GGGAGCAACAGCAGATATCAG 58.508 52.381 5.32 0.00 0.00 2.90
3309 3658 1.141657 GGGGAGCAACAGCAGATATCA 59.858 52.381 5.32 0.00 0.00 2.15
3312 3661 0.833287 GAGGGGAGCAACAGCAGATA 59.167 55.000 0.00 0.00 0.00 1.98
3313 3662 1.203441 TGAGGGGAGCAACAGCAGAT 61.203 55.000 0.00 0.00 0.00 2.90
3314 3663 1.203441 ATGAGGGGAGCAACAGCAGA 61.203 55.000 0.00 0.00 0.00 4.26
3315 3664 0.323178 AATGAGGGGAGCAACAGCAG 60.323 55.000 0.00 0.00 0.00 4.24
3316 3665 0.322816 GAATGAGGGGAGCAACAGCA 60.323 55.000 0.00 0.00 0.00 4.41
3317 3666 0.034670 AGAATGAGGGGAGCAACAGC 60.035 55.000 0.00 0.00 0.00 4.40
3318 3667 1.558756 AGAGAATGAGGGGAGCAACAG 59.441 52.381 0.00 0.00 0.00 3.16
3319 3668 1.661463 AGAGAATGAGGGGAGCAACA 58.339 50.000 0.00 0.00 0.00 3.33
3320 3669 2.797177 AAGAGAATGAGGGGAGCAAC 57.203 50.000 0.00 0.00 0.00 4.17
3321 3670 3.814504 AAAAGAGAATGAGGGGAGCAA 57.185 42.857 0.00 0.00 0.00 3.91
3322 3671 3.814504 AAAAAGAGAATGAGGGGAGCA 57.185 42.857 0.00 0.00 0.00 4.26
3345 3694 9.557061 GGTTTATAGTTAAGAATACAAGGGGAG 57.443 37.037 0.00 0.00 0.00 4.30
3346 3695 8.206189 CGGTTTATAGTTAAGAATACAAGGGGA 58.794 37.037 0.00 0.00 0.00 4.81
3347 3696 8.206189 TCGGTTTATAGTTAAGAATACAAGGGG 58.794 37.037 0.00 0.00 0.00 4.79
3348 3697 9.603921 TTCGGTTTATAGTTAAGAATACAAGGG 57.396 33.333 0.00 0.00 0.00 3.95
3355 3704 9.367444 CACACTCTTCGGTTTATAGTTAAGAAT 57.633 33.333 0.00 0.00 0.00 2.40
3356 3705 7.816031 CCACACTCTTCGGTTTATAGTTAAGAA 59.184 37.037 0.00 0.00 0.00 2.52
3357 3706 7.177216 TCCACACTCTTCGGTTTATAGTTAAGA 59.823 37.037 0.00 0.00 0.00 2.10
3358 3707 7.318141 TCCACACTCTTCGGTTTATAGTTAAG 58.682 38.462 0.00 0.00 0.00 1.85
3359 3708 7.230849 TCCACACTCTTCGGTTTATAGTTAA 57.769 36.000 0.00 0.00 0.00 2.01
3360 3709 6.839124 TCCACACTCTTCGGTTTATAGTTA 57.161 37.500 0.00 0.00 0.00 2.24
3361 3710 5.733620 TCCACACTCTTCGGTTTATAGTT 57.266 39.130 0.00 0.00 0.00 2.24
3362 3711 5.733620 TTCCACACTCTTCGGTTTATAGT 57.266 39.130 0.00 0.00 0.00 2.12
3363 3712 6.164176 AGTTTCCACACTCTTCGGTTTATAG 58.836 40.000 0.00 0.00 0.00 1.31
3364 3713 6.105397 AGTTTCCACACTCTTCGGTTTATA 57.895 37.500 0.00 0.00 0.00 0.98
3365 3714 4.969484 AGTTTCCACACTCTTCGGTTTAT 58.031 39.130 0.00 0.00 0.00 1.40
3366 3715 4.411256 AGTTTCCACACTCTTCGGTTTA 57.589 40.909 0.00 0.00 0.00 2.01
3367 3716 3.277142 AGTTTCCACACTCTTCGGTTT 57.723 42.857 0.00 0.00 0.00 3.27
3368 3717 3.277142 AAGTTTCCACACTCTTCGGTT 57.723 42.857 0.00 0.00 0.00 4.44
3369 3718 3.277142 AAAGTTTCCACACTCTTCGGT 57.723 42.857 0.00 0.00 0.00 4.69
3370 3719 4.351192 CAAAAAGTTTCCACACTCTTCGG 58.649 43.478 0.00 0.00 0.00 4.30
3371 3720 3.791353 GCAAAAAGTTTCCACACTCTTCG 59.209 43.478 0.00 0.00 0.00 3.79
3372 3721 4.998788 AGCAAAAAGTTTCCACACTCTTC 58.001 39.130 0.00 0.00 0.00 2.87
3373 3722 5.405935 AAGCAAAAAGTTTCCACACTCTT 57.594 34.783 0.00 0.00 0.00 2.85
3374 3723 4.998788 GAAGCAAAAAGTTTCCACACTCT 58.001 39.130 0.00 0.00 31.92 3.24
3382 3731 4.094294 GGGTTGTTGGAAGCAAAAAGTTTC 59.906 41.667 0.00 0.00 36.79 2.78
3383 3732 4.006989 GGGTTGTTGGAAGCAAAAAGTTT 58.993 39.130 0.00 0.00 0.00 2.66
3384 3733 3.605634 GGGTTGTTGGAAGCAAAAAGTT 58.394 40.909 0.00 0.00 0.00 2.66
3385 3734 2.093181 GGGGTTGTTGGAAGCAAAAAGT 60.093 45.455 0.00 0.00 0.00 2.66
3386 3735 2.093235 TGGGGTTGTTGGAAGCAAAAAG 60.093 45.455 0.00 0.00 0.00 2.27
3387 3736 1.909302 TGGGGTTGTTGGAAGCAAAAA 59.091 42.857 0.00 0.00 0.00 1.94
3388 3737 1.573108 TGGGGTTGTTGGAAGCAAAA 58.427 45.000 0.00 0.00 0.00 2.44
3389 3738 1.415659 CATGGGGTTGTTGGAAGCAAA 59.584 47.619 0.00 0.00 0.00 3.68
3390 3739 1.047002 CATGGGGTTGTTGGAAGCAA 58.953 50.000 0.00 0.00 0.00 3.91
3391 3740 0.105760 ACATGGGGTTGTTGGAAGCA 60.106 50.000 0.00 0.00 0.00 3.91
3392 3741 1.917872 TACATGGGGTTGTTGGAAGC 58.082 50.000 0.00 0.00 0.00 3.86
3393 3742 5.011533 TCAAATTACATGGGGTTGTTGGAAG 59.988 40.000 0.00 0.00 0.00 3.46
3394 3743 4.901849 TCAAATTACATGGGGTTGTTGGAA 59.098 37.500 0.00 0.00 0.00 3.53
3395 3744 4.282195 GTCAAATTACATGGGGTTGTTGGA 59.718 41.667 0.00 0.00 0.00 3.53
3396 3745 4.562552 GGTCAAATTACATGGGGTTGTTGG 60.563 45.833 0.00 0.00 0.00 3.77
3397 3746 4.283212 AGGTCAAATTACATGGGGTTGTTG 59.717 41.667 0.00 0.00 0.00 3.33
3398 3747 4.488770 AGGTCAAATTACATGGGGTTGTT 58.511 39.130 0.00 0.00 0.00 2.83
3399 3748 4.086457 GAGGTCAAATTACATGGGGTTGT 58.914 43.478 0.00 0.00 0.00 3.32
3400 3749 4.158394 CAGAGGTCAAATTACATGGGGTTG 59.842 45.833 0.00 0.00 0.00 3.77
3401 3750 4.344104 CAGAGGTCAAATTACATGGGGTT 58.656 43.478 0.00 0.00 0.00 4.11
3402 3751 3.309121 CCAGAGGTCAAATTACATGGGGT 60.309 47.826 0.00 0.00 0.00 4.95
3403 3752 3.290710 CCAGAGGTCAAATTACATGGGG 58.709 50.000 0.00 0.00 0.00 4.96
3404 3753 3.968265 ACCAGAGGTCAAATTACATGGG 58.032 45.455 0.00 0.00 0.00 4.00
3417 3766 2.238319 TAGCCCGGATGACCAGAGGT 62.238 60.000 0.73 0.00 39.44 3.85
3418 3767 1.457643 TAGCCCGGATGACCAGAGG 60.458 63.158 0.73 0.00 35.59 3.69
3419 3768 1.742768 GTAGCCCGGATGACCAGAG 59.257 63.158 0.73 0.00 35.59 3.35
3420 3769 2.125326 CGTAGCCCGGATGACCAGA 61.125 63.158 0.73 0.00 35.59 3.86
3421 3770 2.417516 CGTAGCCCGGATGACCAG 59.582 66.667 0.73 0.00 35.59 4.00
3430 3779 1.209127 CAAAACAAGCCGTAGCCCG 59.791 57.895 0.00 0.00 41.25 6.13
3431 3780 0.955905 TTCAAAACAAGCCGTAGCCC 59.044 50.000 0.00 0.00 41.25 5.19
3432 3781 2.595386 CATTCAAAACAAGCCGTAGCC 58.405 47.619 0.00 0.00 41.25 3.93
3433 3782 1.985684 GCATTCAAAACAAGCCGTAGC 59.014 47.619 0.00 0.00 40.32 3.58
3434 3783 3.281341 TGCATTCAAAACAAGCCGTAG 57.719 42.857 0.00 0.00 0.00 3.51
3435 3784 3.254411 TCATGCATTCAAAACAAGCCGTA 59.746 39.130 0.00 0.00 0.00 4.02
3436 3785 2.035704 TCATGCATTCAAAACAAGCCGT 59.964 40.909 0.00 0.00 0.00 5.68
3437 3786 2.664568 CTCATGCATTCAAAACAAGCCG 59.335 45.455 0.00 0.00 0.00 5.52
3438 3787 2.997986 CCTCATGCATTCAAAACAAGCC 59.002 45.455 0.00 0.00 0.00 4.35
3439 3788 2.414138 GCCTCATGCATTCAAAACAAGC 59.586 45.455 0.00 0.00 40.77 4.01
3452 3801 2.812591 CAGACCATTATCTGCCTCATGC 59.187 50.000 0.00 0.00 39.77 4.06
3461 3810 6.721208 TGAAAGAAAAAGGCAGACCATTATCT 59.279 34.615 0.00 0.00 39.06 1.98
3462 3811 6.924111 TGAAAGAAAAAGGCAGACCATTATC 58.076 36.000 0.00 0.00 39.06 1.75
3463 3812 6.916360 TGAAAGAAAAAGGCAGACCATTAT 57.084 33.333 0.00 0.00 39.06 1.28
3464 3813 6.723298 TTGAAAGAAAAAGGCAGACCATTA 57.277 33.333 0.00 0.00 39.06 1.90
3465 3814 5.612725 TTGAAAGAAAAAGGCAGACCATT 57.387 34.783 0.00 0.00 39.06 3.16
3466 3815 5.612725 TTTGAAAGAAAAAGGCAGACCAT 57.387 34.783 0.00 0.00 39.06 3.55
3467 3816 5.413309 TTTTGAAAGAAAAAGGCAGACCA 57.587 34.783 0.00 0.00 39.06 4.02
3551 3901 9.836864 TCTCATACTACAAATACAGCATGATTT 57.163 29.630 0.00 0.00 39.69 2.17
3612 3970 3.016736 AGCCGTGAAAATCTTGTATGGG 58.983 45.455 0.00 0.00 0.00 4.00
3613 3971 3.731867 GCAGCCGTGAAAATCTTGTATGG 60.732 47.826 0.00 0.00 0.00 2.74
3614 3972 3.127548 AGCAGCCGTGAAAATCTTGTATG 59.872 43.478 0.00 0.00 0.00 2.39
3615 3973 3.347216 AGCAGCCGTGAAAATCTTGTAT 58.653 40.909 0.00 0.00 0.00 2.29
3616 3974 2.742053 GAGCAGCCGTGAAAATCTTGTA 59.258 45.455 0.00 0.00 0.00 2.41
3617 3975 1.537202 GAGCAGCCGTGAAAATCTTGT 59.463 47.619 0.00 0.00 0.00 3.16
3618 3976 1.536766 TGAGCAGCCGTGAAAATCTTG 59.463 47.619 0.00 0.00 0.00 3.02
3619 3977 1.896220 TGAGCAGCCGTGAAAATCTT 58.104 45.000 0.00 0.00 0.00 2.40
3621 3979 4.558538 ATTATGAGCAGCCGTGAAAATC 57.441 40.909 0.00 0.00 0.00 2.17
3622 3980 4.989279 AATTATGAGCAGCCGTGAAAAT 57.011 36.364 0.00 0.00 0.00 1.82
3623 3981 4.484236 CAAATTATGAGCAGCCGTGAAAA 58.516 39.130 0.00 0.00 0.00 2.29
3662 4028 4.201763 CGAGTCTACTAACTAACACCGACC 60.202 50.000 0.00 0.00 0.00 4.79
3665 4031 3.686726 ACCGAGTCTACTAACTAACACCG 59.313 47.826 0.00 0.00 0.00 4.94
3705 4071 6.429692 TCTTTCGCACTGGAAATTATTCAGAA 59.570 34.615 8.87 0.00 37.29 3.02
4042 4439 3.564053 AACGGGGAAAAACTGTCAGTA 57.436 42.857 5.77 0.00 0.00 2.74
4099 4502 0.108804 ACTTCCACGCATCCACGTAG 60.109 55.000 0.00 0.00 46.34 3.51
4209 4612 0.676782 ACTACCGTGCTTGGGATTGC 60.677 55.000 0.00 0.00 0.00 3.56
4213 4616 1.229082 AGGACTACCGTGCTTGGGA 60.229 57.895 0.00 0.00 38.86 4.37
4223 4626 0.749454 CCCAAGCATGCAGGACTACC 60.749 60.000 25.58 0.00 0.00 3.18
4338 4742 5.557866 TCTTTTTGGACTAGGAAAGCCTAC 58.442 41.667 0.00 0.00 44.74 3.18
4347 4751 4.072839 GTTCCCACTCTTTTTGGACTAGG 58.927 47.826 0.00 0.00 36.02 3.02
4394 4798 5.008613 GGTGCAAGAATGAACAGTAGACAAA 59.991 40.000 0.00 0.00 36.75 2.83
4445 4849 1.008995 TGCGCAAAACGGAAGCTTC 60.009 52.632 18.54 18.54 40.11 3.86
4453 4857 2.527487 GCTGAAAGATATGCGCAAAACG 59.473 45.455 17.11 0.00 40.64 3.60
4465 4869 4.153117 GTCAGTTGATTGTCGCTGAAAGAT 59.847 41.667 0.00 0.00 39.33 2.40
4472 4876 5.940192 TTTAATGTCAGTTGATTGTCGCT 57.060 34.783 0.00 0.00 0.00 4.93
4514 4919 7.041098 CCAGGCTGTATCATAAAAAGGATACAC 60.041 40.741 14.43 7.64 46.51 2.90
4535 4941 4.215827 CAGCTAAAATGAGATCATCCAGGC 59.784 45.833 0.00 0.34 35.10 4.85
4590 6382 3.517296 TGGAAAAATACCAGCCTGACA 57.483 42.857 0.00 0.00 33.22 3.58
4630 6458 7.123247 GCACCCTGCAAATATTATGATTCCTAT 59.877 37.037 0.00 0.00 44.26 2.57
4675 6503 1.464997 CAGGCGAAGGTTTCTAGCAAC 59.535 52.381 0.00 0.00 0.00 4.17
4678 7116 1.809684 AACAGGCGAAGGTTTCTAGC 58.190 50.000 0.00 0.00 0.00 3.42
4716 7154 5.009854 TCAAAAGAAGAAAAAGTGCAGGG 57.990 39.130 0.00 0.00 0.00 4.45
4717 7155 6.642540 GGTATCAAAAGAAGAAAAAGTGCAGG 59.357 38.462 0.00 0.00 0.00 4.85
4718 7156 7.202526 TGGTATCAAAAGAAGAAAAAGTGCAG 58.797 34.615 0.00 0.00 0.00 4.41
4719 7157 7.106439 TGGTATCAAAAGAAGAAAAAGTGCA 57.894 32.000 0.00 0.00 0.00 4.57
4720 7158 8.419076 TTTGGTATCAAAAGAAGAAAAAGTGC 57.581 30.769 0.00 0.00 39.64 4.40
4721 7159 9.801873 TCTTTGGTATCAAAAGAAGAAAAAGTG 57.198 29.630 2.19 0.00 41.70 3.16
4724 7162 9.313118 GCTTCTTTGGTATCAAAAGAAGAAAAA 57.687 29.630 28.65 5.42 42.49 1.94
4725 7163 7.926018 GGCTTCTTTGGTATCAAAAGAAGAAAA 59.074 33.333 28.65 5.95 42.49 2.29
4729 7167 6.385033 CAGGCTTCTTTGGTATCAAAAGAAG 58.615 40.000 23.89 23.89 42.59 2.85
4732 7170 4.488879 GCAGGCTTCTTTGGTATCAAAAG 58.511 43.478 2.19 0.00 41.70 2.27
4739 7177 3.981308 GCGCAGGCTTCTTTGGTA 58.019 55.556 0.30 0.00 35.83 3.25
4755 7193 6.811665 ACTAAAGAAAACAGGTGAAAACAAGC 59.188 34.615 0.00 0.00 0.00 4.01
4798 7239 3.458189 AGACAACTTCCAACTTCTCACG 58.542 45.455 0.00 0.00 0.00 4.35
4884 7332 1.053264 AAACAACCCTGGCAATGGCA 61.053 50.000 9.67 9.67 43.71 4.92
4907 7355 8.306038 CAACCATCCTCTTTCATCATAAACAAA 58.694 33.333 0.00 0.00 0.00 2.83
4929 7377 3.889538 AGGAAGACAAAGCTAAACCAACC 59.110 43.478 0.00 0.00 0.00 3.77
4931 7379 8.789762 GTTATTAGGAAGACAAAGCTAAACCAA 58.210 33.333 0.00 0.00 0.00 3.67
4933 7381 8.563123 AGTTATTAGGAAGACAAAGCTAAACC 57.437 34.615 0.00 0.00 0.00 3.27
4935 7383 9.379791 GCTAGTTATTAGGAAGACAAAGCTAAA 57.620 33.333 0.00 0.00 0.00 1.85
4960 7409 2.618241 TGACGCTGGGAATATTTGATGC 59.382 45.455 0.00 0.00 0.00 3.91
4976 7425 4.152625 GTGCCGCTGTCATGACGC 62.153 66.667 23.80 23.80 0.00 5.19
5057 7506 5.236478 CGGAATTCGGAAAATATGCACTACT 59.764 40.000 7.20 0.00 34.75 2.57
5058 7507 5.235616 TCGGAATTCGGAAAATATGCACTAC 59.764 40.000 12.85 0.00 39.77 2.73
5059 7508 5.235616 GTCGGAATTCGGAAAATATGCACTA 59.764 40.000 16.39 0.00 39.77 2.74
5121 7570 9.692749 AATCTTCATGATGTTAATGATTGATGC 57.307 29.630 8.33 0.00 34.14 3.91
5144 7593 9.624697 CAGAATAGAACTACTAGCATCTCAATC 57.375 37.037 0.00 0.00 34.35 2.67


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

AutoCloner maintained by Alex Coulton.