Multiple sequence alignment - TraesCS3D01G407400

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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 TraesCS3D01G407400 chr3D 100.000 8630 0 0 1 8630 520718226 520726855 0.000000e+00 15937.0
1 TraesCS3D01G407400 chr3D 92.511 227 17 0 6936 7162 520724939 520725165 8.350000e-85 326.0
2 TraesCS3D01G407400 chr3D 92.511 227 17 0 6714 6940 520725161 520725387 8.350000e-85 326.0
3 TraesCS3D01G407400 chr3D 86.047 129 14 4 4490 4615 93257380 93257507 1.510000e-27 135.0
4 TraesCS3D01G407400 chr3A 91.807 4406 172 74 1 4305 656104603 656108920 0.000000e+00 5962.0
5 TraesCS3D01G407400 chr3A 94.971 3261 124 14 4594 7835 656109235 656112474 0.000000e+00 5077.0
6 TraesCS3D01G407400 chr3A 89.440 464 34 6 8168 8630 656114618 656115067 9.720000e-159 571.0
7 TraesCS3D01G407400 chr3A 97.890 237 5 0 4359 4595 656108916 656109152 2.240000e-110 411.0
8 TraesCS3D01G407400 chr3A 88.412 233 21 1 6714 6940 656111567 656111799 8.530000e-70 276.0
9 TraesCS3D01G407400 chr3A 88.889 216 10 7 7823 8037 656113093 656113295 4.000000e-63 254.0
10 TraesCS3D01G407400 chr3A 91.573 178 14 1 1406 1583 661842067 661841891 2.410000e-60 244.0
11 TraesCS3D01G407400 chr3A 89.032 155 15 2 4377 4529 531452017 531452171 3.180000e-44 191.0
12 TraesCS3D01G407400 chr3A 95.082 61 3 0 8036 8096 656114558 656114618 7.130000e-16 97.1
13 TraesCS3D01G407400 chr3A 100.000 50 0 0 4566 4615 142577567 142577616 9.220000e-15 93.5
14 TraesCS3D01G407400 chr3B 87.851 2634 143 72 18 2580 686341201 686343728 0.000000e+00 2928.0
15 TraesCS3D01G407400 chr3B 93.557 1878 94 16 4609 6479 686345546 686347403 0.000000e+00 2772.0
16 TraesCS3D01G407400 chr3B 92.372 1324 76 8 6505 7806 686347402 686348722 0.000000e+00 1862.0
17 TraesCS3D01G407400 chr3B 94.341 1025 30 11 2608 3616 686343718 686344730 0.000000e+00 1546.0
18 TraesCS3D01G407400 chr3B 91.719 797 37 5 3606 4381 686344763 686345551 0.000000e+00 1079.0
19 TraesCS3D01G407400 chr3B 92.347 392 21 3 7825 8208 686348706 686349096 4.550000e-152 549.0
20 TraesCS3D01G407400 chr3B 88.462 130 12 3 4490 4618 555504550 555504677 4.170000e-33 154.0
21 TraesCS3D01G407400 chr3B 94.118 51 3 0 4369 4419 61536183 61536233 2.580000e-10 78.7
22 TraesCS3D01G407400 chr5B 87.500 600 64 7 1208 1804 68814394 68814985 0.000000e+00 682.0
23 TraesCS3D01G407400 chr5B 87.898 157 17 1 4378 4532 418373542 418373386 5.320000e-42 183.0
24 TraesCS3D01G407400 chr5B 95.238 42 1 1 4377 4417 166686059 166686100 2.010000e-06 65.8
25 TraesCS3D01G407400 chr2B 92.798 361 20 5 1446 1804 461896028 461895672 1.280000e-142 518.0
26 TraesCS3D01G407400 chr2B 96.053 76 3 0 1324 1399 767953446 767953371 3.270000e-24 124.0
27 TraesCS3D01G407400 chr2B 91.026 78 7 0 4490 4567 25347404 25347481 1.180000e-18 106.0
28 TraesCS3D01G407400 chr2B 91.837 49 3 1 4366 4414 224650730 224650777 5.590000e-07 67.6
29 TraesCS3D01G407400 chr7D 89.175 194 19 2 1207 1399 549768596 549768788 3.110000e-59 241.0
30 TraesCS3D01G407400 chr7D 86.719 128 9 6 4490 4617 91339962 91339843 1.510000e-27 135.0
31 TraesCS3D01G407400 chr7D 92.308 78 6 0 4490 4567 449339772 449339695 2.550000e-20 111.0
32 TraesCS3D01G407400 chr7B 82.917 240 23 9 511 748 624700737 624700514 5.280000e-47 200.0
33 TraesCS3D01G407400 chr6A 85.864 191 23 2 4379 4567 75913762 75913574 5.280000e-47 200.0
34 TraesCS3D01G407400 chr6A 89.796 49 2 3 4364 4410 100354360 100354407 9.360000e-05 60.2
35 TraesCS3D01G407400 chr4B 83.246 191 24 4 4380 4567 126324476 126324661 1.490000e-37 169.0
36 TraesCS3D01G407400 chr4B 80.412 194 30 7 4380 4567 466965714 466965905 3.250000e-29 141.0
37 TraesCS3D01G407400 chr4B 92.308 78 6 0 4490 4567 362014492 362014569 2.550000e-20 111.0
38 TraesCS3D01G407400 chr7A 83.333 174 25 2 18 190 657422610 657422440 3.230000e-34 158.0
39 TraesCS3D01G407400 chr7A 96.591 88 3 0 1717 1804 49629856 49629943 6.980000e-31 147.0
40 TraesCS3D01G407400 chr7A 92.727 55 3 1 4364 4418 15776208 15776155 2.580000e-10 78.7
41 TraesCS3D01G407400 chr6D 86.301 146 18 2 1255 1399 469343766 469343622 3.230000e-34 158.0
42 TraesCS3D01G407400 chr6D 87.692 130 12 1 4490 4615 34338191 34338062 1.940000e-31 148.0
43 TraesCS3D01G407400 chr6D 97.143 35 1 0 4376 4410 365730104 365730070 9.360000e-05 60.2
44 TraesCS3D01G407400 chr5D 92.000 100 6 1 4397 4494 558970533 558970434 1.170000e-28 139.0
45 TraesCS3D01G407400 chr4D 91.089 101 7 1 4399 4497 110081031 110080931 1.510000e-27 135.0
46 TraesCS3D01G407400 chr1A 89.720 107 10 1 4390 4496 484329961 484330066 1.510000e-27 135.0
47 TraesCS3D01G407400 chrUn 98.413 63 1 0 1720 1782 433056979 433056917 2.550000e-20 111.0
48 TraesCS3D01G407400 chr2A 87.500 72 5 4 4568 4638 778431060 778430992 7.180000e-11 80.5
49 TraesCS3D01G407400 chr5A 86.111 72 8 2 4358 4428 662382361 662382291 9.290000e-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 TraesCS3D01G407400 chr3D 520718226 520726855 8629 False 5529.666667 15937 95.007333 1 8630 3 chr3D.!!$F2 8629
1 TraesCS3D01G407400 chr3A 656104603 656115067 10464 False 1806.871429 5962 92.355857 1 8630 7 chr3A.!!$F3 8629
2 TraesCS3D01G407400 chr3B 686341201 686349096 7895 False 1789.333333 2928 92.031167 18 8208 6 chr3B.!!$F3 8190
3 TraesCS3D01G407400 chr5B 68814394 68814985 591 False 682.000000 682 87.500000 1208 1804 1 chr5B.!!$F1 596

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
197 201 0.028242 CGACGACTTCCTCCTGATCG 59.972 60.000 0.00 0.00 38.71 3.69 F
428 452 0.106894 GCTTGCTTATAGTCCGGGCT 59.893 55.000 15.76 15.76 0.00 5.19 F
1937 2058 0.175989 GAACGCCTTAGGTGAGGAGG 59.824 60.000 19.64 0.00 40.49 4.30 F
1962 2083 0.722282 GCGGCCGTTTGTTTTGTTTT 59.278 45.000 28.70 0.00 0.00 2.43 F
2125 2246 1.018226 CAGGTGCTGCTTTCTCTCGG 61.018 60.000 0.00 0.00 0.00 4.63 F
2818 2950 1.923204 CTGTCGCACTATCAACTGCTC 59.077 52.381 0.00 0.00 0.00 4.26 F
4411 4621 2.954792 TCCTAAATACTCCCTCCGTCC 58.045 52.381 0.00 0.00 0.00 4.79 F
5261 5560 1.421268 TGTGAAGGAGCCACTTGATGT 59.579 47.619 0.00 0.00 35.66 3.06 F
5962 6265 0.178990 GGGCTGTGAAACTGGGAACT 60.179 55.000 0.00 0.00 38.04 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2083 0.038251 CACGGCAGAACTAGTGCAGA 60.038 55.000 3.00 0.00 43.12 4.26 R
1975 2096 0.531974 GAACAACAGAGGACACGGCA 60.532 55.000 0.00 0.00 0.00 5.69 R
3806 3995 2.040412 GACTCCCTCCAGAACCAACAAT 59.960 50.000 0.00 0.00 0.00 2.71 R
4012 4201 8.196103 GTCCGAATGGTCTAGTTATAACTTCTT 58.804 37.037 22.66 8.17 37.19 2.52 R
4114 4323 8.294577 AGAAGGTTGTACGTTTCCAATAAAATC 58.705 33.333 0.00 0.00 0.00 2.17 R
4840 5139 1.100510 CTGGGTCCTGCATGTTGATG 58.899 55.000 0.00 0.00 0.00 3.07 R
5585 5884 0.179100 CACTGCCCAGTCATACCGAG 60.179 60.000 0.00 0.00 40.20 4.63 R
6688 6997 0.388134 TTCTGTGCTTACGCGGAGAC 60.388 55.000 12.47 8.83 42.48 3.36 R
7921 8897 0.609151 CAAGCATGCCATCCCACAAA 59.391 50.000 15.66 0.00 0.00 2.83 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 35 1.001378 CACACAAGCTGCCCTGTAAAC 60.001 52.381 4.83 0.00 0.00 2.01
46 48 4.982295 GCCCTGTAAACTGACATGTTTTTC 59.018 41.667 0.00 0.00 40.23 2.29
122 126 1.201965 GCGATCAAAGAGCTGAAACGG 60.202 52.381 0.00 0.00 33.17 4.44
159 163 0.458025 CAAGTACTCGGCGTTCCTCC 60.458 60.000 6.85 0.00 0.00 4.30
160 164 0.611340 AAGTACTCGGCGTTCCTCCT 60.611 55.000 6.85 0.00 0.00 3.69
161 165 1.031029 AGTACTCGGCGTTCCTCCTC 61.031 60.000 6.85 0.00 0.00 3.71
175 179 4.148825 CCTCGCTTCCCAGTCCCG 62.149 72.222 0.00 0.00 0.00 5.14
197 201 0.028242 CGACGACTTCCTCCTGATCG 59.972 60.000 0.00 0.00 38.71 3.69
215 223 4.041938 TGATCGATCCATCCATCCATCAAA 59.958 41.667 22.31 0.00 30.22 2.69
248 256 0.316204 GTGACAGGCTGCAAAGCATT 59.684 50.000 15.89 0.00 38.13 3.56
261 269 1.744368 AGCATTGCTGACTGCTCCG 60.744 57.895 11.09 0.00 45.30 4.63
351 360 1.342975 TGTAGTGGCATCCTAGGCAGA 60.343 52.381 2.96 0.00 45.31 4.26
360 369 0.183014 TCCTAGGCAGACGAGTAGGG 59.817 60.000 2.96 0.00 33.98 3.53
361 370 1.457009 CCTAGGCAGACGAGTAGGGC 61.457 65.000 0.00 0.00 0.00 5.19
362 371 0.466555 CTAGGCAGACGAGTAGGGCT 60.467 60.000 0.00 7.58 39.64 5.19
392 416 7.186128 CGCATGTAAATCTGTATAACTTGCAA 58.814 34.615 0.00 0.00 39.71 4.08
413 437 5.331902 CAAGTATACGGTGGATTTTGCTTG 58.668 41.667 0.00 0.00 0.00 4.01
414 438 2.939460 ATACGGTGGATTTTGCTTGC 57.061 45.000 0.00 0.00 0.00 4.01
415 439 1.904287 TACGGTGGATTTTGCTTGCT 58.096 45.000 0.00 0.00 0.00 3.91
416 440 1.039856 ACGGTGGATTTTGCTTGCTT 58.960 45.000 0.00 0.00 0.00 3.91
417 441 2.235016 ACGGTGGATTTTGCTTGCTTA 58.765 42.857 0.00 0.00 0.00 3.09
418 442 2.825532 ACGGTGGATTTTGCTTGCTTAT 59.174 40.909 0.00 0.00 0.00 1.73
419 443 4.013728 ACGGTGGATTTTGCTTGCTTATA 58.986 39.130 0.00 0.00 0.00 0.98
420 444 4.096382 ACGGTGGATTTTGCTTGCTTATAG 59.904 41.667 0.00 0.00 0.00 1.31
421 445 4.096382 CGGTGGATTTTGCTTGCTTATAGT 59.904 41.667 0.00 0.00 0.00 2.12
422 446 5.582550 GGTGGATTTTGCTTGCTTATAGTC 58.417 41.667 0.00 0.00 0.00 2.59
423 447 5.450550 GGTGGATTTTGCTTGCTTATAGTCC 60.451 44.000 0.00 0.00 0.00 3.85
424 448 4.335315 TGGATTTTGCTTGCTTATAGTCCG 59.665 41.667 0.00 0.00 0.00 4.79
425 449 4.261197 GGATTTTGCTTGCTTATAGTCCGG 60.261 45.833 0.00 0.00 0.00 5.14
426 450 2.325583 TTGCTTGCTTATAGTCCGGG 57.674 50.000 0.00 0.00 0.00 5.73
427 451 0.179056 TGCTTGCTTATAGTCCGGGC 60.179 55.000 0.00 0.00 0.00 6.13
428 452 0.106894 GCTTGCTTATAGTCCGGGCT 59.893 55.000 15.76 15.76 0.00 5.19
429 453 1.871080 CTTGCTTATAGTCCGGGCTG 58.129 55.000 21.58 1.97 0.00 4.85
430 454 1.412710 CTTGCTTATAGTCCGGGCTGA 59.587 52.381 21.58 3.01 0.00 4.26
431 455 1.040646 TGCTTATAGTCCGGGCTGAG 58.959 55.000 21.58 14.84 0.00 3.35
432 456 0.318762 GCTTATAGTCCGGGCTGAGG 59.681 60.000 21.58 8.27 0.00 3.86
433 457 1.996798 CTTATAGTCCGGGCTGAGGA 58.003 55.000 21.58 0.00 34.99 3.71
503 544 2.546368 TCCGTGTCAATTTCCAAGTTCG 59.454 45.455 0.00 0.00 0.00 3.95
506 547 1.265635 TGTCAATTTCCAAGTTCGCCG 59.734 47.619 0.00 0.00 0.00 6.46
580 634 2.873133 TTTGTTTCGCCGAAAATGGT 57.127 40.000 14.64 0.00 33.14 3.55
599 656 2.433239 GGTAAGGCATCTTCGTTAGGGA 59.567 50.000 0.00 0.00 34.59 4.20
639 696 1.319669 GAACTGATCGCCGTTACGTTC 59.680 52.381 3.52 0.00 33.44 3.95
644 701 2.801679 TGATCGCCGTTACGTTCTTTTT 59.198 40.909 3.52 0.00 33.86 1.94
648 714 5.341407 TCGCCGTTACGTTCTTTTTAAAT 57.659 34.783 3.52 0.00 0.00 1.40
658 724 4.618067 CGTTCTTTTTAAATGGCCGTTACC 59.382 41.667 11.50 0.00 0.00 2.85
673 739 4.619863 GCCGTTACCTATTTCTGTGACTGA 60.620 45.833 0.00 0.00 0.00 3.41
677 743 6.349445 CGTTACCTATTTCTGTGACTGAGAGT 60.349 42.308 0.00 0.00 0.00 3.24
682 748 3.494045 TTCTGTGACTGAGAGTATGCG 57.506 47.619 0.00 0.00 0.00 4.73
688 754 2.826128 TGACTGAGAGTATGCGGTTCTT 59.174 45.455 0.00 0.00 0.00 2.52
689 755 3.119459 TGACTGAGAGTATGCGGTTCTTC 60.119 47.826 0.00 0.00 0.00 2.87
690 756 3.093057 ACTGAGAGTATGCGGTTCTTCT 58.907 45.455 0.00 0.00 0.00 2.85
757 826 3.517602 TCGCGTAGTTAGTTACCGACTA 58.482 45.455 5.77 0.00 39.86 2.59
885 977 3.701604 CTTTCGACGCTCCCTCCCG 62.702 68.421 0.00 0.00 0.00 5.14
900 992 4.814294 CCGTCCCCTTCGCCTTCG 62.814 72.222 0.00 0.00 0.00 3.79
906 998 2.820037 CCTTCGCCTTCGCCTTCC 60.820 66.667 0.00 0.00 35.26 3.46
907 999 2.266055 CTTCGCCTTCGCCTTCCT 59.734 61.111 0.00 0.00 35.26 3.36
909 1001 2.232298 CTTCGCCTTCGCCTTCCTCT 62.232 60.000 0.00 0.00 35.26 3.69
910 1002 2.507110 TTCGCCTTCGCCTTCCTCTG 62.507 60.000 0.00 0.00 35.26 3.35
911 1003 2.821810 GCCTTCGCCTTCCTCTGC 60.822 66.667 0.00 0.00 0.00 4.26
913 1005 2.664081 CCTTCGCCTTCCTCTGCCT 61.664 63.158 0.00 0.00 0.00 4.75
914 1006 1.449246 CTTCGCCTTCCTCTGCCTG 60.449 63.158 0.00 0.00 0.00 4.85
915 1007 3.612247 TTCGCCTTCCTCTGCCTGC 62.612 63.158 0.00 0.00 0.00 4.85
918 1010 4.093291 CCTTCCTCTGCCTGCGCT 62.093 66.667 9.73 0.00 35.36 5.92
919 1011 2.511145 CTTCCTCTGCCTGCGCTC 60.511 66.667 9.73 0.00 35.36 5.03
920 1012 2.999648 TTCCTCTGCCTGCGCTCT 61.000 61.111 9.73 0.00 35.36 4.09
921 1013 2.904470 CTTCCTCTGCCTGCGCTCTC 62.904 65.000 9.73 0.00 35.36 3.20
922 1014 4.869440 CCTCTGCCTGCGCTCTCG 62.869 72.222 9.73 0.00 39.07 4.04
923 1015 3.819920 CTCTGCCTGCGCTCTCGA 61.820 66.667 9.73 0.00 38.10 4.04
1055 1158 4.806481 CGATGCCGTCGTCGTCGT 62.806 66.667 9.58 0.00 45.19 4.34
1057 1160 3.378331 GATGCCGTCGTCGTCGTCT 62.378 63.158 10.76 0.00 38.33 4.18
1060 1163 4.157958 CCGTCGTCGTCGTCTCCC 62.158 72.222 10.76 0.00 38.33 4.30
1429 1550 2.202492 CTCCCGCAGTTCGAGTCG 60.202 66.667 6.09 6.09 41.67 4.18
1936 2057 0.895530 TGAACGCCTTAGGTGAGGAG 59.104 55.000 19.64 0.00 41.75 3.69
1937 2058 0.175989 GAACGCCTTAGGTGAGGAGG 59.824 60.000 19.64 0.00 40.49 4.30
1939 2060 2.501610 GCCTTAGGTGAGGAGGCG 59.498 66.667 0.00 0.00 45.64 5.52
1940 2061 2.359967 GCCTTAGGTGAGGAGGCGT 61.360 63.158 0.00 0.00 45.64 5.68
1941 2062 1.817209 CCTTAGGTGAGGAGGCGTC 59.183 63.158 0.00 0.00 39.25 5.19
1942 2063 1.677637 CCTTAGGTGAGGAGGCGTCC 61.678 65.000 17.88 17.88 44.33 4.79
1962 2083 0.722282 GCGGCCGTTTGTTTTGTTTT 59.278 45.000 28.70 0.00 0.00 2.43
1966 2087 2.222931 GGCCGTTTGTTTTGTTTTCTGC 60.223 45.455 0.00 0.00 0.00 4.26
1975 2096 6.509418 TGTTTTGTTTTCTGCACTAGTTCT 57.491 33.333 0.00 0.00 0.00 3.01
1992 2113 1.069765 CTGCCGTGTCCTCTGTTGT 59.930 57.895 0.00 0.00 0.00 3.32
1996 2117 1.784525 CCGTGTCCTCTGTTGTTCTC 58.215 55.000 0.00 0.00 0.00 2.87
2004 2125 3.144506 CCTCTGTTGTTCTCACTGCATT 58.855 45.455 0.00 0.00 0.00 3.56
2012 2133 2.880890 GTTCTCACTGCATTGTGGTTCT 59.119 45.455 3.77 0.00 38.40 3.01
2125 2246 1.018226 CAGGTGCTGCTTTCTCTCGG 61.018 60.000 0.00 0.00 0.00 4.63
2395 2525 4.819630 TCATGTCCAAAACCTGTAGTTGTC 59.180 41.667 0.00 0.00 39.19 3.18
2407 2537 7.312415 ACCTGTAGTTGTCTTAAACATAGGT 57.688 36.000 0.00 0.00 37.82 3.08
2502 2633 4.374843 TGTTTATGCATCTTGACATGGC 57.625 40.909 0.19 0.00 0.00 4.40
2523 2654 2.029728 CGCCTTCGTCAATTCATCTCAC 59.970 50.000 0.00 0.00 0.00 3.51
2579 2710 7.793927 TGTGTATTTGTAGTGAACACATGAA 57.206 32.000 0.00 0.00 43.90 2.57
2582 2713 7.172532 GTGTATTTGTAGTGAACACATGAAGGA 59.827 37.037 0.00 0.00 40.08 3.36
2794 2926 2.309755 AGCCTCAATCAATCAACCTCCA 59.690 45.455 0.00 0.00 0.00 3.86
2795 2927 3.053095 AGCCTCAATCAATCAACCTCCAT 60.053 43.478 0.00 0.00 0.00 3.41
2818 2950 1.923204 CTGTCGCACTATCAACTGCTC 59.077 52.381 0.00 0.00 0.00 4.26
2920 3054 3.009473 TCTGTTAGCTTCCTGCCTCAATT 59.991 43.478 0.00 0.00 44.23 2.32
3159 3299 9.930158 TTAAAGTAGCCCTGGTTTAATGATATT 57.070 29.630 0.00 0.00 0.00 1.28
3883 4072 8.536172 CCAATGGTGGCATTCTACGTAAGTTG 62.536 46.154 0.00 0.00 44.32 3.16
4012 4201 9.832445 AAGTTCTTGAAGTAGTCAACAGATTAA 57.168 29.630 0.00 0.00 41.47 1.40
4114 4323 3.056393 TGCAGATTTGGCCTTCTGATTTG 60.056 43.478 25.56 10.93 41.53 2.32
4132 4341 9.834628 TCTGATTTGATTTTATTGGAAACGTAC 57.165 29.630 0.00 0.00 0.00 3.67
4304 4514 6.093909 GGAAAATGGGCCACTTGATAAATTTG 59.906 38.462 9.28 0.00 0.00 2.32
4336 4546 8.991783 AAGTCATTCTTGTGATGGATATGAAT 57.008 30.769 0.00 0.00 34.77 2.57
4338 4548 9.722184 AGTCATTCTTGTGATGGATATGAATAG 57.278 33.333 0.00 0.00 0.00 1.73
4339 4549 9.499479 GTCATTCTTGTGATGGATATGAATAGT 57.501 33.333 0.00 0.00 0.00 2.12
4411 4621 2.954792 TCCTAAATACTCCCTCCGTCC 58.045 52.381 0.00 0.00 0.00 4.79
4448 4658 6.430000 TCTCAAGCTTAGTACAATTTTGGACC 59.570 38.462 0.00 0.00 43.16 4.46
4469 4679 5.910614 ACCGAAGTTAGTACAAAGTTGACT 58.089 37.500 0.00 0.58 0.00 3.41
4541 4751 6.250711 TGGACCACATACGGATGTATATAGT 58.749 40.000 14.23 6.13 44.82 2.12
4840 5139 7.918536 ATCTGATGCAATGTATGTATTCCTC 57.081 36.000 0.00 0.00 34.17 3.71
4880 5179 4.330620 CAGTTTTGAACCATATGGCAATGC 59.669 41.667 22.18 12.94 39.32 3.56
4939 5238 2.548493 GCTCCTGATCTTCTGGCATCTC 60.548 54.545 0.00 0.00 35.69 2.75
4947 5246 2.707791 TCTTCTGGCATCTCCTTATGGG 59.292 50.000 0.00 0.00 35.26 4.00
5144 5443 5.058008 GTGTTCGCACAAGAAACAAATATCG 59.942 40.000 0.00 0.00 46.85 2.92
5261 5560 1.421268 TGTGAAGGAGCCACTTGATGT 59.579 47.619 0.00 0.00 35.66 3.06
5264 5563 2.106338 TGAAGGAGCCACTTGATGTCAA 59.894 45.455 0.00 0.00 0.00 3.18
5274 5573 1.872952 CTTGATGTCAACGGTGCAGAA 59.127 47.619 0.00 0.00 0.00 3.02
5285 5584 2.420022 ACGGTGCAGAAAATGATGCTAC 59.580 45.455 0.00 0.00 42.98 3.58
5451 5750 1.962807 CAACTCCAAGCAATTGGTGGA 59.037 47.619 13.73 17.83 42.62 4.02
5504 5803 1.669779 GCCATCAAGCTGCTTACTCAG 59.330 52.381 15.51 2.30 37.15 3.35
5584 5883 7.093988 GCATCCTCTCTAATGCTTCATCTACTA 60.094 40.741 0.28 0.00 43.87 1.82
5585 5884 7.753309 TCCTCTCTAATGCTTCATCTACTAC 57.247 40.000 0.00 0.00 0.00 2.73
5586 5885 7.522542 TCCTCTCTAATGCTTCATCTACTACT 58.477 38.462 0.00 0.00 0.00 2.57
5686 5987 3.852286 ACTCGCATCAACGTTGGTAATA 58.148 40.909 27.02 8.77 0.00 0.98
5950 6253 0.242825 CAAGCAGTGATTGGGCTGTG 59.757 55.000 13.36 0.00 38.04 3.66
5953 6256 0.961019 GCAGTGATTGGGCTGTGAAA 59.039 50.000 0.00 0.00 35.33 2.69
5962 6265 0.178990 GGGCTGTGAAACTGGGAACT 60.179 55.000 0.00 0.00 38.04 3.01
6198 6501 6.038050 CCATTCCTAGCTCAGAGAATTGAAAC 59.962 42.308 0.00 0.00 0.00 2.78
6269 6572 8.999431 CCAAAAGAAAGAGTAGCACTATAACAA 58.001 33.333 0.00 0.00 0.00 2.83
6397 6703 2.358737 GCTGAAGTGTCCCACCCG 60.359 66.667 0.00 0.00 34.49 5.28
6398 6704 2.347490 CTGAAGTGTCCCACCCGG 59.653 66.667 0.00 0.00 34.49 5.73
6424 6730 2.203294 GCAGTGGTTCCCCGTGTT 60.203 61.111 0.00 0.00 0.00 3.32
6486 6792 5.302313 CAGAGATGACAGAAGAGGATGATGA 59.698 44.000 0.00 0.00 0.00 2.92
6513 6819 2.200337 GCCGTCCAAAGCCAAAGGT 61.200 57.895 0.00 0.00 0.00 3.50
6514 6820 1.956802 CCGTCCAAAGCCAAAGGTC 59.043 57.895 0.00 0.00 0.00 3.85
6531 6837 0.721718 GTCACTTCCCATTCGCGAAG 59.278 55.000 27.20 17.68 41.08 3.79
6583 6889 4.326548 GCAAAGAAGCAAATGAAGATGAGC 59.673 41.667 0.00 0.00 0.00 4.26
6603 6912 3.009916 AGCAAAGGAGACAAGATGATGGT 59.990 43.478 0.00 0.00 0.00 3.55
6619 6928 1.398692 TGGTTCCAACTGCTCCAAAC 58.601 50.000 0.00 0.00 0.00 2.93
6625 6934 1.197721 CCAACTGCTCCAAACGATGAC 59.802 52.381 0.00 0.00 0.00 3.06
6688 6997 1.446907 CTGCCACTAAGCTGGAGTTG 58.553 55.000 0.00 0.00 32.30 3.16
6865 7174 0.390492 CCCTGCATGAGCTCGACATA 59.610 55.000 9.64 0.00 42.74 2.29
6982 7291 0.821711 CTACAGGAGAGGAGAGGGCG 60.822 65.000 0.00 0.00 0.00 6.13
7006 7321 1.340657 GAGATCATCCGATGCGCGTC 61.341 60.000 19.84 19.84 38.67 5.19
7022 7337 1.342082 CGTCGAAGGGTACACTTGCG 61.342 60.000 16.88 17.59 0.00 4.85
7023 7338 1.012486 GTCGAAGGGTACACTTGCGG 61.012 60.000 16.88 4.45 0.00 5.69
7024 7339 2.388232 CGAAGGGTACACTTGCGGC 61.388 63.158 16.88 0.00 0.00 6.53
7031 7346 0.457853 GTACACTTGCGGCATCGAGA 60.458 55.000 2.28 0.00 39.00 4.04
7099 7414 1.153369 CGACATCTGCCCGGTCAAT 60.153 57.895 0.00 0.00 0.00 2.57
7321 7636 1.953559 TTGTATCAGATTCCAGCCGC 58.046 50.000 0.00 0.00 0.00 6.53
7327 7642 1.074775 AGATTCCAGCCGCCACAAA 59.925 52.632 0.00 0.00 0.00 2.83
7385 7700 4.082895 CCAAGACATGAAGCAGGAGAAAAG 60.083 45.833 0.00 0.00 0.00 2.27
7511 7827 7.480760 ACAATGGGTGTGCTTTATTTTCTAT 57.519 32.000 0.00 0.00 39.72 1.98
7684 8018 5.136828 TGTGTTAACCTTTGTGACATGGAT 58.863 37.500 11.24 3.30 0.00 3.41
7689 8023 7.336679 TGTTAACCTTTGTGACATGGATGATAG 59.663 37.037 11.24 0.00 0.00 2.08
7711 8045 5.581605 AGTTTTGCTGCGGTGATTATTATG 58.418 37.500 0.00 0.00 0.00 1.90
7785 8123 2.244651 GCCGCGATGGTATGGTGAC 61.245 63.158 8.23 0.00 41.21 3.67
7800 8138 2.135933 GGTGACACTGTAGTTGTGAGC 58.864 52.381 5.39 0.00 38.65 4.26
7801 8139 2.224066 GGTGACACTGTAGTTGTGAGCT 60.224 50.000 5.39 0.00 38.65 4.09
7802 8140 3.053455 GTGACACTGTAGTTGTGAGCTC 58.947 50.000 6.82 6.82 38.65 4.09
7803 8141 2.287608 TGACACTGTAGTTGTGAGCTCG 60.288 50.000 9.64 0.00 38.65 5.03
7828 8166 1.537669 TTTTTGTGCCGGGGGTAGT 59.462 52.632 2.18 0.00 0.00 2.73
7862 8832 1.185618 AGGCGGTAGTGCACAGAAGA 61.186 55.000 21.04 0.00 36.28 2.87
7893 8863 2.100631 CGTTGGCTGTCGTGGATCC 61.101 63.158 4.20 4.20 0.00 3.36
7987 8963 0.191064 AGACTTGGGAGTGGGACTGA 59.809 55.000 0.00 0.00 35.88 3.41
8099 10339 1.071814 TGCACCCCGTACCAAGTTC 59.928 57.895 0.00 0.00 0.00 3.01
8109 10349 3.875134 CCGTACCAAGTTCTGTTTCAACT 59.125 43.478 0.00 0.00 35.51 3.16
8119 10359 5.586643 AGTTCTGTTTCAACTTCAGTCCTTC 59.413 40.000 0.00 0.00 29.29 3.46
8121 10361 4.876107 TCTGTTTCAACTTCAGTCCTTCAC 59.124 41.667 0.00 0.00 0.00 3.18
8122 10362 3.945285 TGTTTCAACTTCAGTCCTTCACC 59.055 43.478 0.00 0.00 0.00 4.02
8124 10364 3.753294 TCAACTTCAGTCCTTCACCTC 57.247 47.619 0.00 0.00 0.00 3.85
8144 10386 7.383029 TCACCTCTTGTATTTACTACACGTTTG 59.617 37.037 0.00 0.00 40.06 2.93
8208 10450 4.736126 AATTTGCCCAGTGCCTATTAAC 57.264 40.909 0.00 0.00 40.16 2.01
8216 10458 4.161565 CCCAGTGCCTATTAACACTCACTA 59.838 45.833 0.00 0.00 45.15 2.74
8219 10461 6.924060 CCAGTGCCTATTAACACTCACTATAC 59.076 42.308 0.00 0.00 45.15 1.47
8225 10467 8.601476 GCCTATTAACACTCACTATACAAACAC 58.399 37.037 0.00 0.00 0.00 3.32
8227 10469 9.647797 CTATTAACACTCACTATACAAACACCA 57.352 33.333 0.00 0.00 0.00 4.17
8242 10484 5.465724 ACAAACACCAGAAAAGAGATCGTAC 59.534 40.000 0.00 0.00 0.00 3.67
8247 10489 5.926542 CACCAGAAAAGAGATCGTACTCAAA 59.073 40.000 12.28 0.00 39.14 2.69
8280 10522 0.846427 TCACCTCCCCTGCCAAGAAT 60.846 55.000 0.00 0.00 0.00 2.40
8342 10585 2.400399 TCTTTAGGAGAAACGTGTGCG 58.600 47.619 0.00 0.00 44.93 5.34
8357 10600 2.853594 GTGTGCGTGCATATTTTCATGG 59.146 45.455 0.00 0.00 0.00 3.66
8364 10607 5.932021 GTGCATATTTTCATGGACGAAAC 57.068 39.130 0.00 0.00 37.48 2.78
8365 10608 5.398169 GTGCATATTTTCATGGACGAAACA 58.602 37.500 0.00 0.00 37.48 2.83
8371 10614 8.586273 CATATTTTCATGGACGAAACAACATTC 58.414 33.333 0.00 0.00 34.68 2.67
8413 10656 0.647410 GGAACAGTCATGCATCGACG 59.353 55.000 17.74 15.49 38.46 5.12
8428 10671 0.585357 CGACGTATACTCCCTCCGTG 59.415 60.000 0.56 0.00 0.00 4.94
8429 10672 1.673168 GACGTATACTCCCTCCGTGT 58.327 55.000 0.56 0.00 0.00 4.49
8441 10684 5.130477 ACTCCCTCCGTGTTTCATAATATGT 59.870 40.000 0.00 0.00 0.00 2.29
8451 10694 5.641636 TGTTTCATAATATGTCGTGCACACT 59.358 36.000 18.64 7.03 38.04 3.55
8470 10713 6.433766 CACACTTTTTGTTTTTCAAAGGCAA 58.566 32.000 0.00 0.00 45.14 4.52
8471 10714 6.914757 CACACTTTTTGTTTTTCAAAGGCAAA 59.085 30.769 0.00 0.00 45.14 3.68
8472 10715 6.915300 ACACTTTTTGTTTTTCAAAGGCAAAC 59.085 30.769 1.99 0.00 45.14 2.93
8473 10716 6.086110 CACTTTTTGTTTTTCAAAGGCAAACG 59.914 34.615 1.99 0.00 45.14 3.60
8474 10717 5.674933 TTTTGTTTTTCAAAGGCAAACGT 57.325 30.435 1.99 0.00 45.14 3.99
8475 10718 4.653806 TTGTTTTTCAAAGGCAAACGTG 57.346 36.364 0.00 0.00 33.81 4.49
8476 10719 3.120511 TTGTTTTTCAAAGGCAAACGTGC 60.121 39.130 0.00 0.00 40.53 5.34
8559 10802 7.933577 ACGTAGTTCATGATGAATATGGTGATT 59.066 33.333 11.46 0.00 37.78 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 13 2.410322 TACAGGGCAGCTTGTGTGGG 62.410 60.000 11.81 0.00 0.00 4.61
53 57 2.348779 CGCAAAGAATGGCTGCAAAAAC 60.349 45.455 0.50 0.00 35.78 2.43
122 126 2.436115 GCCCGCTCCACCTTGTAC 60.436 66.667 0.00 0.00 0.00 2.90
159 163 4.148825 CCGGGACTGGGAAGCGAG 62.149 72.222 0.00 0.00 0.00 5.03
175 179 3.069318 AGGAGGAAGTCGTCGCCC 61.069 66.667 0.00 0.00 0.00 6.13
197 201 5.047519 GGATTGTTTGATGGATGGATGGATC 60.048 44.000 0.00 0.00 0.00 3.36
215 223 2.420547 CCTGTCACCGATGATGGATTGT 60.421 50.000 0.00 0.00 37.14 2.71
261 269 2.325857 GATGACGATGCCAAGCGC 59.674 61.111 0.00 0.00 39.29 5.92
313 322 7.758980 GCCACTACAGATCATCATTATCTACTG 59.241 40.741 0.00 0.00 32.40 2.74
361 370 1.202065 ACAGATTTACATGCGCGCAAG 60.202 47.619 39.68 35.64 43.44 4.01
362 371 0.801872 ACAGATTTACATGCGCGCAA 59.198 45.000 39.68 22.49 0.00 4.85
392 416 3.377172 GCAAGCAAAATCCACCGTATACT 59.623 43.478 0.56 0.00 0.00 2.12
413 437 0.318762 CCTCAGCCCGGACTATAAGC 59.681 60.000 0.73 0.00 0.00 3.09
414 438 1.614413 GTCCTCAGCCCGGACTATAAG 59.386 57.143 0.73 0.00 45.87 1.73
415 439 1.700955 GTCCTCAGCCCGGACTATAA 58.299 55.000 0.73 0.00 45.87 0.98
416 440 3.434053 GTCCTCAGCCCGGACTATA 57.566 57.895 0.73 0.00 45.87 1.31
417 441 4.279326 GTCCTCAGCCCGGACTAT 57.721 61.111 0.73 0.00 45.87 2.12
424 448 0.251787 AAAATGTGGGTCCTCAGCCC 60.252 55.000 0.00 0.00 46.26 5.19
425 449 1.273327 CAAAAATGTGGGTCCTCAGCC 59.727 52.381 0.00 0.00 41.06 4.85
426 450 1.963515 ACAAAAATGTGGGTCCTCAGC 59.036 47.619 0.00 0.00 0.00 4.26
427 451 3.304659 CGAACAAAAATGTGGGTCCTCAG 60.305 47.826 0.00 0.00 0.00 3.35
428 452 2.621055 CGAACAAAAATGTGGGTCCTCA 59.379 45.455 0.00 0.00 0.00 3.86
429 453 2.621526 ACGAACAAAAATGTGGGTCCTC 59.378 45.455 0.00 0.00 0.00 3.71
430 454 2.661718 ACGAACAAAAATGTGGGTCCT 58.338 42.857 0.00 0.00 0.00 3.85
431 455 4.571372 TTACGAACAAAAATGTGGGTCC 57.429 40.909 0.00 0.00 0.00 4.46
432 456 6.267070 TCTTTTACGAACAAAAATGTGGGTC 58.733 36.000 0.00 0.00 0.00 4.46
433 457 6.210287 TCTTTTACGAACAAAAATGTGGGT 57.790 33.333 0.00 0.00 0.00 4.51
434 458 6.975772 TCTTCTTTTACGAACAAAAATGTGGG 59.024 34.615 0.00 0.00 0.00 4.61
514 565 4.888326 TGATTGATTCAACCAAAAGGGG 57.112 40.909 0.15 0.00 42.91 4.79
572 626 4.965119 ACGAAGATGCCTTACCATTTTC 57.035 40.909 0.00 0.00 34.65 2.29
580 634 4.829872 TTTCCCTAACGAAGATGCCTTA 57.170 40.909 0.00 0.00 31.62 2.69
604 661 6.681777 CGATCAGTTCCATTTTCCTTTCTTT 58.318 36.000 0.00 0.00 0.00 2.52
606 663 4.156739 GCGATCAGTTCCATTTTCCTTTCT 59.843 41.667 0.00 0.00 0.00 2.52
607 664 4.415735 GCGATCAGTTCCATTTTCCTTTC 58.584 43.478 0.00 0.00 0.00 2.62
620 677 1.068055 AGAACGTAACGGCGATCAGTT 60.068 47.619 16.62 14.28 36.37 3.16
625 682 4.988708 TTAAAAAGAACGTAACGGCGAT 57.011 36.364 16.62 3.59 35.59 4.58
626 683 4.785669 TTTAAAAAGAACGTAACGGCGA 57.214 36.364 16.62 0.00 35.59 5.54
639 696 8.248253 AGAAATAGGTAACGGCCATTTAAAAAG 58.752 33.333 2.24 0.00 46.39 2.27
644 701 5.587043 CACAGAAATAGGTAACGGCCATTTA 59.413 40.000 2.24 0.00 46.39 1.40
648 714 2.568062 TCACAGAAATAGGTAACGGCCA 59.432 45.455 2.24 0.00 46.39 5.36
658 724 5.685068 CGCATACTCTCAGTCACAGAAATAG 59.315 44.000 0.00 0.00 0.00 1.73
673 739 1.405821 CGGAGAAGAACCGCATACTCT 59.594 52.381 0.00 0.00 43.74 3.24
706 772 1.441016 CTTTCTCGCTTGCGGTTGC 60.441 57.895 15.10 0.00 43.20 4.17
775 844 4.961511 TCACTGTGACCGTGCGCC 62.962 66.667 6.36 0.00 32.54 6.53
776 845 3.702555 GTCACTGTGACCGTGCGC 61.703 66.667 26.50 0.00 41.37 6.09
777 846 2.279186 TGTCACTGTGACCGTGCG 60.279 61.111 31.58 0.00 46.40 5.34
779 848 1.956170 GCCTGTCACTGTGACCGTG 60.956 63.158 31.58 22.00 46.40 4.94
782 851 2.357517 CCGCCTGTCACTGTGACC 60.358 66.667 31.58 18.65 46.40 4.02
806 879 0.320508 GAGTCTTGGGTGGGTCGTTC 60.321 60.000 0.00 0.00 0.00 3.95
901 993 4.093291 AGCGCAGGCAGAGGAAGG 62.093 66.667 11.47 0.00 43.41 3.46
903 995 2.999648 AGAGCGCAGGCAGAGGAA 61.000 61.111 11.47 0.00 43.41 3.36
906 998 3.819920 TCGAGAGCGCAGGCAGAG 61.820 66.667 11.47 0.00 43.41 3.35
907 999 4.121669 GTCGAGAGCGCAGGCAGA 62.122 66.667 11.47 0.00 43.41 4.26
915 1007 3.479269 GGGTTTGCGTCGAGAGCG 61.479 66.667 0.00 0.00 37.44 5.03
916 1008 3.119096 GGGGTTTGCGTCGAGAGC 61.119 66.667 0.00 5.91 0.00 4.09
917 1009 2.434359 GGGGGTTTGCGTCGAGAG 60.434 66.667 0.00 0.00 0.00 3.20
918 1010 4.367023 CGGGGGTTTGCGTCGAGA 62.367 66.667 0.00 0.00 0.00 4.04
1336 1448 1.982938 GAGGTACTGGTGGCGGACT 60.983 63.158 0.00 0.00 41.55 3.85
1925 2046 2.050350 CGGACGCCTCCTCACCTAA 61.050 63.158 0.07 0.00 33.79 2.69
1939 2060 3.472736 AAAACAAACGGCCGCGGAC 62.473 57.895 33.48 29.37 0.00 4.79
1940 2061 3.210528 AAAACAAACGGCCGCGGA 61.211 55.556 33.48 0.00 0.00 5.54
1941 2062 3.027449 CAAAACAAACGGCCGCGG 61.027 61.111 28.58 24.05 0.00 6.46
1942 2063 1.414527 AAACAAAACAAACGGCCGCG 61.415 50.000 28.58 17.14 0.00 6.46
1943 2064 0.722282 AAAACAAAACAAACGGCCGC 59.278 45.000 28.58 0.00 0.00 6.53
1944 2065 2.028643 CAGAAAACAAAACAAACGGCCG 59.971 45.455 26.86 26.86 0.00 6.13
1946 2067 2.413453 TGCAGAAAACAAAACAAACGGC 59.587 40.909 0.00 0.00 0.00 5.68
1947 2068 3.677596 AGTGCAGAAAACAAAACAAACGG 59.322 39.130 0.00 0.00 0.00 4.44
1948 2069 4.901866 AGTGCAGAAAACAAAACAAACG 57.098 36.364 0.00 0.00 0.00 3.60
1949 2070 6.944557 ACTAGTGCAGAAAACAAAACAAAC 57.055 33.333 0.00 0.00 0.00 2.93
1950 2071 7.328249 CAGAACTAGTGCAGAAAACAAAACAAA 59.672 33.333 3.00 0.00 0.00 2.83
1951 2072 6.806249 CAGAACTAGTGCAGAAAACAAAACAA 59.194 34.615 3.00 0.00 0.00 2.83
1952 2073 6.321717 CAGAACTAGTGCAGAAAACAAAACA 58.678 36.000 3.00 0.00 0.00 2.83
1953 2074 5.230097 GCAGAACTAGTGCAGAAAACAAAAC 59.770 40.000 3.00 0.00 40.86 2.43
1954 2075 5.339990 GCAGAACTAGTGCAGAAAACAAAA 58.660 37.500 3.00 0.00 40.86 2.44
1955 2076 4.202010 GGCAGAACTAGTGCAGAAAACAAA 60.202 41.667 3.00 0.00 43.12 2.83
1962 2083 0.038251 CACGGCAGAACTAGTGCAGA 60.038 55.000 3.00 0.00 43.12 4.26
1966 2087 0.603569 AGGACACGGCAGAACTAGTG 59.396 55.000 0.00 0.00 40.17 2.74
1975 2096 0.531974 GAACAACAGAGGACACGGCA 60.532 55.000 0.00 0.00 0.00 5.69
1992 2113 2.880268 CAGAACCACAATGCAGTGAGAA 59.120 45.455 22.73 0.00 42.05 2.87
1996 2117 1.069703 CGACAGAACCACAATGCAGTG 60.070 52.381 13.51 13.51 39.21 3.66
2004 2125 0.865111 CGCAATTCGACAGAACCACA 59.135 50.000 0.00 0.00 39.48 4.17
2012 2133 0.882484 TTCTGCACCGCAATTCGACA 60.882 50.000 0.00 0.00 38.41 4.35
2117 2238 4.812091 TCAAATCGTTCAAAACCGAGAGAA 59.188 37.500 0.00 0.00 36.41 2.87
2122 2243 4.752604 TGAGATCAAATCGTTCAAAACCGA 59.247 37.500 0.00 0.00 37.51 4.69
2125 2246 9.214953 GTATCATGAGATCAAATCGTTCAAAAC 57.785 33.333 0.09 0.00 35.67 2.43
2188 2314 1.799258 CTGCACCAACCTGTTCCAGC 61.799 60.000 0.00 0.00 0.00 4.85
2310 2436 3.829948 CATCAACCAGAAATGCAGTGTC 58.170 45.455 0.00 0.00 0.00 3.67
2355 2481 1.761449 TGATGTTTGGCACACACTGT 58.239 45.000 8.90 0.00 40.12 3.55
2407 2537 5.990386 TGCTTGCAAAAATCATCTAGCAAAA 59.010 32.000 0.00 0.00 40.87 2.44
2502 2633 2.029728 GTGAGATGAATTGACGAAGGCG 59.970 50.000 0.00 0.00 44.79 5.52
2523 2654 3.646324 GCATATTGCACACCTGCCTAGG 61.646 54.545 3.67 3.67 45.95 3.02
2552 2683 6.460664 TGTGTTCACTACAAATACACATCG 57.539 37.500 0.00 0.00 42.78 3.84
2582 2713 1.668419 GCATGCCATAGGAACGAGTT 58.332 50.000 6.36 0.00 0.00 3.01
2595 2727 1.275856 TCAGTTTTCCAATGGCATGCC 59.724 47.619 30.54 30.54 0.00 4.40
2656 2788 6.780031 TGGTCCACATGGGGTTATTATAAATG 59.220 38.462 15.27 0.00 37.22 2.32
2818 2950 3.494626 ACATTGACAGTGCAAGTTCGTAG 59.505 43.478 0.00 0.00 0.00 3.51
3159 3299 4.104102 ACTTCCTTTCATGGTTACCAGACA 59.896 41.667 10.74 0.42 36.75 3.41
3793 3982 7.363530 CCAGAACCAACAATCTGATCATTGATT 60.364 37.037 14.50 9.62 44.64 2.57
3806 3995 2.040412 GACTCCCTCCAGAACCAACAAT 59.960 50.000 0.00 0.00 0.00 2.71
4012 4201 8.196103 GTCCGAATGGTCTAGTTATAACTTCTT 58.804 37.037 22.66 8.17 37.19 2.52
4114 4323 8.294577 AGAAGGTTGTACGTTTCCAATAAAATC 58.705 33.333 0.00 0.00 0.00 2.17
4132 4341 9.528018 TTAGCTGTGAAATTTTAAAGAAGGTTG 57.472 29.630 4.37 0.00 0.00 3.77
4304 4514 7.370383 TCCATCACAAGAATGACTTAAAAAGC 58.630 34.615 0.00 0.00 37.03 3.51
4411 4621 7.440523 ACTAAGCTTGAGACACTTATTTTGG 57.559 36.000 9.86 0.00 0.00 3.28
4448 4658 7.695869 AAGAGTCAACTTTGTACTAACTTCG 57.304 36.000 0.00 0.00 0.00 3.79
4469 4679 5.796502 ATTCCCTCTGTCCCAAAATAAGA 57.203 39.130 0.00 0.00 0.00 2.10
4840 5139 1.100510 CTGGGTCCTGCATGTTGATG 58.899 55.000 0.00 0.00 0.00 3.07
4880 5179 3.118112 AGGTCCAGCATCAGGAAGTATTG 60.118 47.826 0.00 0.00 36.80 1.90
4939 5238 2.092646 TGTCCGGTTGATTCCCATAAGG 60.093 50.000 0.00 0.00 0.00 2.69
4947 5246 2.972625 TCATCAGTGTCCGGTTGATTC 58.027 47.619 0.00 0.00 29.48 2.52
5144 5443 4.193826 TGAGACAGTGCCATCTTAAGTC 57.806 45.455 1.63 0.00 0.00 3.01
5261 5560 2.351641 GCATCATTTTCTGCACCGTTGA 60.352 45.455 0.00 0.00 38.28 3.18
5264 5563 1.538047 AGCATCATTTTCTGCACCGT 58.462 45.000 0.00 0.00 40.88 4.83
5274 5573 4.496341 GCGCTGTTACATGTAGCATCATTT 60.496 41.667 20.85 0.00 37.29 2.32
5285 5584 1.399440 AGATTGCAGCGCTGTTACATG 59.601 47.619 35.80 12.76 0.00 3.21
5451 5750 5.885912 ACGACATAAAAGAATAACATGGGCT 59.114 36.000 0.00 0.00 0.00 5.19
5504 5803 0.379316 TGCATTGCACTCGATCATGC 59.621 50.000 7.38 9.76 42.40 4.06
5543 5842 3.030291 AGGATGCCACAAGTTCAAAACA 58.970 40.909 0.00 0.00 0.00 2.83
5584 5883 0.614979 ACTGCCCAGTCATACCGAGT 60.615 55.000 0.00 0.00 36.92 4.18
5585 5884 0.179100 CACTGCCCAGTCATACCGAG 60.179 60.000 0.00 0.00 40.20 4.63
5586 5885 1.613317 CCACTGCCCAGTCATACCGA 61.613 60.000 0.00 0.00 40.20 4.69
5643 5942 9.767684 CGAGTATAATGTGCTTTTGAACAATAA 57.232 29.630 0.00 0.00 42.14 1.40
5644 5943 7.908082 GCGAGTATAATGTGCTTTTGAACAATA 59.092 33.333 0.00 0.00 42.14 1.90
5645 5944 6.747280 GCGAGTATAATGTGCTTTTGAACAAT 59.253 34.615 0.00 0.00 42.14 2.71
5686 5987 9.010029 ACAACAGGTCTAAATTTAATTCGTGAT 57.990 29.630 16.24 7.80 0.00 3.06
5950 6253 9.152595 CTGTAGTAAAGATTAGTTCCCAGTTTC 57.847 37.037 0.00 0.00 0.00 2.78
5953 6256 7.612677 CACTGTAGTAAAGATTAGTTCCCAGT 58.387 38.462 0.00 0.00 0.00 4.00
5962 6265 7.065803 GCCAGATTTGCACTGTAGTAAAGATTA 59.934 37.037 0.00 0.00 34.04 1.75
6253 6556 8.712285 TTGGTACATTTGTTATAGTGCTACTC 57.288 34.615 0.00 0.00 39.30 2.59
6269 6572 7.442062 CCTTTTCTTGCTTGATTTTGGTACATT 59.558 33.333 0.00 0.00 39.30 2.71
6424 6730 4.265893 CTCTATCGGCAATCCTAGAGCTA 58.734 47.826 0.00 0.00 33.31 3.32
6453 6759 7.180322 TCTTCTGTCATCTCTGATTTTAGCT 57.820 36.000 0.00 0.00 32.98 3.32
6486 6792 0.962356 CTTTGGACGGCAAGCAGGAT 60.962 55.000 0.00 0.00 0.00 3.24
6489 6795 2.256461 GCTTTGGACGGCAAGCAG 59.744 61.111 8.39 0.00 44.18 4.24
6531 6837 3.157087 TCAATCTTCTTTGGTGGCCTTC 58.843 45.455 3.32 0.00 0.00 3.46
6583 6889 4.397417 GGAACCATCATCTTGTCTCCTTTG 59.603 45.833 0.00 0.00 0.00 2.77
6603 6912 1.879380 CATCGTTTGGAGCAGTTGGAA 59.121 47.619 0.00 0.00 0.00 3.53
6619 6928 2.021068 ATGGGTGCTCCTCGTCATCG 62.021 60.000 4.53 0.00 36.20 3.84
6625 6934 2.202987 GCAGATGGGTGCTCCTCG 60.203 66.667 4.53 0.00 40.54 4.63
6688 6997 0.388134 TTCTGTGCTTACGCGGAGAC 60.388 55.000 12.47 8.83 42.48 3.36
6693 7002 0.666274 TCTGGTTCTGTGCTTACGCG 60.666 55.000 3.53 3.53 39.65 6.01
6945 7254 4.450976 TGTAGCTTTCTTCAGTTGCTTCA 58.549 39.130 0.00 0.00 35.47 3.02
6982 7291 1.155042 GCATCGGATGATCTCTTGGC 58.845 55.000 21.69 0.00 30.49 4.52
7006 7321 2.388232 GCCGCAAGTGTACCCTTCG 61.388 63.158 0.00 0.00 0.00 3.79
7039 7354 3.423645 CCTTTTTCGTGTCGAAGCTCATC 60.424 47.826 4.86 0.00 46.43 2.92
7099 7414 1.140312 AGAACTTCTTCCCACAGCCA 58.860 50.000 0.00 0.00 0.00 4.75
7162 7477 2.432628 CACTTGAGCGGACGGTCC 60.433 66.667 17.38 17.38 41.45 4.46
7201 7516 2.176546 CATGCCCACTTGAACGCG 59.823 61.111 3.53 3.53 0.00 6.01
7321 7636 2.954753 GCCTGTCTCGCGTTTGTGG 61.955 63.158 5.77 5.92 0.00 4.17
7327 7642 4.057428 GAGTGGCCTGTCTCGCGT 62.057 66.667 5.77 0.00 0.00 6.01
7385 7700 6.323203 TGTCGCTTCTAGTATACCATAACC 57.677 41.667 0.00 0.00 0.00 2.85
7511 7827 9.996554 AATGACCAATGATCGTAATTAGATACA 57.003 29.630 0.00 0.00 0.00 2.29
7522 7838 8.993121 GTAATCATAGAAATGACCAATGATCGT 58.007 33.333 0.00 0.00 44.79 3.73
7575 7908 7.568315 CGTCAATACATCAGACATAACATCAGC 60.568 40.741 0.00 0.00 32.68 4.26
7684 8018 2.177394 TCACCGCAGCAAAACTATCA 57.823 45.000 0.00 0.00 0.00 2.15
7689 8023 5.339990 ACATAATAATCACCGCAGCAAAAC 58.660 37.500 0.00 0.00 0.00 2.43
7711 8045 8.902540 ATGGTTTCCCTTCTTTTATTCAAAAC 57.097 30.769 0.00 0.00 30.52 2.43
7744 8078 1.372128 CCGCAGCAAAAGTGGCTTC 60.372 57.895 0.00 0.00 40.23 3.86
7785 8123 2.423926 ACGAGCTCACAACTACAGTG 57.576 50.000 15.40 0.00 38.32 3.66
7813 8151 2.432563 CAACTACCCCCGGCACAA 59.567 61.111 0.00 0.00 0.00 3.33
7814 8152 2.850130 ACAACTACCCCCGGCACA 60.850 61.111 0.00 0.00 0.00 4.57
7828 8166 1.165907 CGCCTCCAACAAGCTCACAA 61.166 55.000 0.00 0.00 0.00 3.33
7862 8832 1.244019 GCCAACGGATCTGTGCCTTT 61.244 55.000 8.25 0.00 0.00 3.11
7893 8863 1.299316 CAGCCCAACAGCACAAACG 60.299 57.895 0.00 0.00 34.23 3.60
7921 8897 0.609151 CAAGCATGCCATCCCACAAA 59.391 50.000 15.66 0.00 0.00 2.83
7987 8963 2.821969 CACCAGGCAGCTATTTCAGTTT 59.178 45.455 0.00 0.00 0.00 2.66
8023 8999 1.486145 TTCAGGAACGGAGGAACCCC 61.486 60.000 0.00 0.00 31.97 4.95
8099 10339 4.035675 GGTGAAGGACTGAAGTTGAAACAG 59.964 45.833 0.00 0.00 37.62 3.16
8109 10349 5.825593 AATACAAGAGGTGAAGGACTGAA 57.174 39.130 0.00 0.00 0.00 3.02
8119 10359 7.170320 ACAAACGTGTAGTAAATACAAGAGGTG 59.830 37.037 8.31 5.89 45.88 4.00
8121 10361 7.507304 CACAAACGTGTAGTAAATACAAGAGG 58.493 38.462 8.31 1.53 45.88 3.69
8122 10362 7.007697 GCACAAACGTGTAGTAAATACAAGAG 58.992 38.462 8.31 2.09 45.88 2.85
8124 10364 6.651308 TGCACAAACGTGTAGTAAATACAAG 58.349 36.000 0.00 1.09 45.88 3.16
8144 10386 5.808403 TCATTTGTTTGATTTTGCTTGCAC 58.192 33.333 0.00 0.00 0.00 4.57
8197 10439 8.601476 GTTTGTATAGTGAGTGTTAATAGGCAC 58.399 37.037 0.00 0.00 35.98 5.01
8208 10450 7.441157 TCTTTTCTGGTGTTTGTATAGTGAGTG 59.559 37.037 0.00 0.00 0.00 3.51
8216 10458 6.231211 ACGATCTCTTTTCTGGTGTTTGTAT 58.769 36.000 0.00 0.00 0.00 2.29
8219 10461 5.696724 AGTACGATCTCTTTTCTGGTGTTTG 59.303 40.000 0.00 0.00 0.00 2.93
8225 10467 6.159988 AGTTTGAGTACGATCTCTTTTCTGG 58.840 40.000 11.33 0.00 35.68 3.86
8227 10469 7.434492 TCAAGTTTGAGTACGATCTCTTTTCT 58.566 34.615 11.33 4.47 35.68 2.52
8342 10585 5.398169 TGTTTCGTCCATGAAAATATGCAC 58.602 37.500 0.00 0.00 39.40 4.57
8364 10607 1.369625 GGGGAGCACTACGAATGTTG 58.630 55.000 0.00 0.00 0.00 3.33
8365 10608 0.108329 CGGGGAGCACTACGAATGTT 60.108 55.000 0.00 0.00 0.00 2.71
8392 10635 1.662629 GTCGATGCATGACTGTTCCAG 59.337 52.381 2.46 0.00 37.52 3.86
8397 10640 2.871182 ATACGTCGATGCATGACTGT 57.129 45.000 19.93 19.55 34.17 3.55
8413 10656 4.667519 ATGAAACACGGAGGGAGTATAC 57.332 45.455 0.00 0.00 0.00 1.47
8428 10671 6.106877 AGTGTGCACGACATATTATGAAAC 57.893 37.500 13.13 0.00 36.78 2.78
8429 10672 6.735678 AAGTGTGCACGACATATTATGAAA 57.264 33.333 13.13 0.00 36.78 2.69
8441 10684 4.299155 TGAAAAACAAAAAGTGTGCACGA 58.701 34.783 13.13 0.00 40.60 4.35
8451 10694 5.909610 CACGTTTGCCTTTGAAAAACAAAAA 59.090 32.000 6.59 0.00 45.97 1.94
8534 10777 7.895975 ATCACCATATTCATCATGAACTACG 57.104 36.000 0.98 0.00 39.45 3.51


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

AutoCloner maintained by Alex Coulton.