Multiple sequence alignment - TraesCS3B01G018600

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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 TraesCS3B01G018600 chr3B 100.000 2678 0 0 1 2678 7615872 7613195 0.000000e+00 4946.0
1 TraesCS3B01G018600 chr3B 100.000 2352 0 0 2955 5306 7612918 7610567 0.000000e+00 4344.0
2 TraesCS3B01G018600 chr3B 86.719 768 77 10 3307 4065 143589313 143588562 0.000000e+00 830.0
3 TraesCS3B01G018600 chr3B 88.079 302 21 9 2160 2459 143589590 143589302 1.410000e-90 344.0
4 TraesCS3B01G018600 chr3B 87.500 256 25 3 3319 3571 458263993 458264244 6.720000e-74 289.0
5 TraesCS3B01G018600 chr3D 89.989 1798 114 25 915 2675 6009141 6010909 0.000000e+00 2263.0
6 TraesCS3B01G018600 chr3D 92.438 1124 61 10 2958 4064 6011028 6012144 0.000000e+00 1583.0
7 TraesCS3B01G018600 chr3D 88.235 1241 106 22 4099 5306 6012296 6013529 0.000000e+00 1447.0
8 TraesCS3B01G018600 chr3D 91.892 518 35 6 1 515 6008162 6008675 0.000000e+00 717.0
9 TraesCS3B01G018600 chr3D 95.122 41 2 0 4060 4100 6012180 6012220 1.230000e-06 65.8
10 TraesCS3B01G018600 chr3A 92.451 1126 64 9 2955 4065 15091117 15089998 0.000000e+00 1589.0
11 TraesCS3B01G018600 chr3A 86.273 1253 94 35 4063 5306 15089960 15088777 0.000000e+00 1290.0
12 TraesCS3B01G018600 chr3A 88.699 876 61 15 915 1776 15092933 15092082 0.000000e+00 1035.0
13 TraesCS3B01G018600 chr3A 89.229 817 56 13 1894 2678 15091958 15091142 0.000000e+00 992.0
14 TraesCS3B01G018600 chr3A 95.652 92 4 0 1771 1862 15092034 15091943 1.190000e-31 148.0
15 TraesCS3B01G018600 chr1A 87.135 754 79 7 3322 4065 514893469 514892724 0.000000e+00 839.0
16 TraesCS3B01G018600 chr1A 87.135 754 79 7 3322 4065 515149734 515148989 0.000000e+00 839.0
17 TraesCS3B01G018600 chr5D 86.569 752 85 6 3322 4065 171684548 171683805 0.000000e+00 815.0
18 TraesCS3B01G018600 chr6D 86.412 758 84 9 3319 4065 300219160 300219909 0.000000e+00 811.0
19 TraesCS3B01G018600 chr7B 86.162 766 76 10 3309 4065 128029384 128030128 0.000000e+00 800.0
20 TraesCS3B01G018600 chr7B 85.789 767 78 13 3309 4065 127750741 127751486 0.000000e+00 784.0
21 TraesCS3B01G018600 chr7B 88.645 273 19 5 2180 2451 128029125 128029386 6.630000e-84 322.0
22 TraesCS3B01G018600 chr7B 87.591 274 21 5 2179 2451 127750482 127750743 6.680000e-79 305.0
23 TraesCS3B01G018600 chr7B 87.097 279 23 6 2182 2459 211418934 211419200 2.400000e-78 303.0
24 TraesCS3B01G018600 chr4B 88.619 536 45 6 3307 3838 659669627 659670150 5.800000e-179 638.0
25 TraesCS3B01G018600 chr2D 90.845 142 9 3 2160 2299 437375867 437375728 2.520000e-43 187.0
26 TraesCS3B01G018600 chr2D 84.302 172 21 5 2970 3137 378094059 378094228 4.250000e-36 163.0
27 TraesCS3B01G018600 chr2D 90.698 43 1 3 1753 1793 576286664 576286705 3.000000e-03 54.7
28 TraesCS3B01G018600 chr2A 84.746 177 24 3 2964 3138 379152419 379152244 1.960000e-39 174.0
29 TraesCS3B01G018600 chr2A 83.240 179 28 2 2955 3132 660499920 660500097 4.250000e-36 163.0
30 TraesCS3B01G018600 chr2A 89.394 66 6 1 4063 4128 720970989 720970925 1.220000e-11 82.4
31 TraesCS3B01G018600 chr1D 84.358 179 22 5 2955 3132 337775362 337775189 2.540000e-38 171.0
32 TraesCS3B01G018600 chr5B 84.181 177 24 4 2964 3137 355610005 355610180 9.140000e-38 169.0
33 TraesCS3B01G018600 chr4D 83.607 183 24 6 2957 3137 431198333 431198511 3.290000e-37 167.0
34 TraesCS3B01G018600 chr6B 82.320 181 27 5 2963 3140 535449859 535449681 9.200000e-33 152.0
35 TraesCS3B01G018600 chr7A 89.231 65 6 1 4064 4128 151765229 151765292 4.410000e-11 80.5


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 TraesCS3B01G018600 chr3B 7610567 7615872 5305 True 4645.00 4946 100.0000 1 5306 2 chr3B.!!$R1 5305
1 TraesCS3B01G018600 chr3B 143588562 143589590 1028 True 587.00 830 87.3990 2160 4065 2 chr3B.!!$R2 1905
2 TraesCS3B01G018600 chr3D 6008162 6013529 5367 False 1215.16 2263 91.5352 1 5306 5 chr3D.!!$F1 5305
3 TraesCS3B01G018600 chr3A 15088777 15092933 4156 True 1010.80 1589 90.4608 915 5306 5 chr3A.!!$R1 4391
4 TraesCS3B01G018600 chr1A 514892724 514893469 745 True 839.00 839 87.1350 3322 4065 1 chr1A.!!$R1 743
5 TraesCS3B01G018600 chr1A 515148989 515149734 745 True 839.00 839 87.1350 3322 4065 1 chr1A.!!$R2 743
6 TraesCS3B01G018600 chr5D 171683805 171684548 743 True 815.00 815 86.5690 3322 4065 1 chr5D.!!$R1 743
7 TraesCS3B01G018600 chr6D 300219160 300219909 749 False 811.00 811 86.4120 3319 4065 1 chr6D.!!$F1 746
8 TraesCS3B01G018600 chr7B 128029125 128030128 1003 False 561.00 800 87.4035 2180 4065 2 chr7B.!!$F3 1885
9 TraesCS3B01G018600 chr7B 127750482 127751486 1004 False 544.50 784 86.6900 2179 4065 2 chr7B.!!$F2 1886
10 TraesCS3B01G018600 chr4B 659669627 659670150 523 False 638.00 638 88.6190 3307 3838 1 chr4B.!!$F1 531

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
510 514 0.038526 CCGCGAGAAGTACAACCTGT 60.039 55.0 8.23 0.00 0.00 4.00 F
1120 1263 0.252193 AGCTGCTCCACCTCTTCTCT 60.252 55.0 0.00 0.00 0.00 3.10 F
1246 1389 0.393808 TAATCCTGGTCTTTGCCGCC 60.394 55.0 0.00 0.00 0.00 6.13 F
2378 2601 0.394762 TTCACCATCTGCCATGGAGC 60.395 55.0 18.40 0.45 41.64 4.70 F
3127 3381 0.109913 GGGGCCTAATAAACCCGGAG 59.890 60.0 0.73 0.00 45.27 4.63 F
4262 4679 0.515564 GTGATTTGGACCGACAACCG 59.484 55.0 0.00 0.00 38.18 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1935 0.031716 TGCTACTCCCTCTGCTCCAT 60.032 55.0 0.00 0.0 0.00 3.41 R
3095 3349 0.032117 AGGCCCCCTCTTATTTTGGC 60.032 55.0 0.00 0.0 38.16 4.52 R
3127 3381 4.338964 GCAGGTCTCTTAACTACTACTCCC 59.661 50.0 0.00 0.0 0.00 4.30 R
4247 4664 0.810823 GACACGGTTGTCGGTCCAAA 60.811 55.0 0.00 0.0 42.86 3.28 R
4750 5189 0.259065 TCATACCCTCAGCGAGACCT 59.741 55.0 7.07 0.0 0.00 3.85 R
5283 5725 0.250234 CGAGGGATGAAGCTCCAACA 59.750 55.0 0.00 0.0 37.01 3.33 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
62 64 1.541620 GGAACCCCTCCTCCAAGGT 60.542 63.158 0.00 0.00 41.61 3.50
123 127 1.341976 ACCCCTCTTTTGCACACAACT 60.342 47.619 0.00 0.00 34.87 3.16
129 133 4.261197 CCTCTTTTGCACACAACTTCTACC 60.261 45.833 0.00 0.00 34.87 3.18
154 158 0.325203 GTTGCCTCCTCCCTCTCTCT 60.325 60.000 0.00 0.00 0.00 3.10
156 160 0.325110 TGCCTCCTCCCTCTCTCTTG 60.325 60.000 0.00 0.00 0.00 3.02
157 161 0.325203 GCCTCCTCCCTCTCTCTTGT 60.325 60.000 0.00 0.00 0.00 3.16
158 162 1.775385 CCTCCTCCCTCTCTCTTGTC 58.225 60.000 0.00 0.00 0.00 3.18
159 163 1.287739 CCTCCTCCCTCTCTCTTGTCT 59.712 57.143 0.00 0.00 0.00 3.41
190 194 1.045407 TGTCTTGTCGTAAGGCTGGT 58.955 50.000 7.93 0.00 46.88 4.00
194 198 0.606604 TTGTCGTAAGGCTGGTCCTC 59.393 55.000 0.00 0.00 46.94 3.71
262 266 2.731691 TTTCAGTGGACTGGGAGCGC 62.732 60.000 0.00 0.00 43.91 5.92
322 326 1.678970 GGCGCACCCTCAGGATTTT 60.679 57.895 10.83 0.00 36.73 1.82
356 360 2.217429 TTTTTCCGGCTTTGCTTGTC 57.783 45.000 0.00 0.00 0.00 3.18
374 378 5.627135 CTTGTCTTTCCCTAGGTTTTGGTA 58.373 41.667 8.29 0.00 0.00 3.25
402 406 4.710324 TCTTTTCTTTTCGGGAAGCAGTA 58.290 39.130 0.00 0.00 0.00 2.74
421 425 5.161358 CAGTACATTTCTACGAGAAGCACA 58.839 41.667 0.00 0.00 35.37 4.57
446 450 4.787551 TGTGCTTACTGAAAAGGGAAAGA 58.212 39.130 0.00 0.00 0.00 2.52
450 454 4.578928 GCTTACTGAAAAGGGAAAGACACA 59.421 41.667 0.00 0.00 0.00 3.72
451 455 5.278022 GCTTACTGAAAAGGGAAAGACACAG 60.278 44.000 0.00 0.00 0.00 3.66
491 495 2.036346 AGAAAAGCCCAACATGTGCTTC 59.964 45.455 18.89 10.19 44.11 3.86
492 496 0.681175 AAAGCCCAACATGTGCTTCC 59.319 50.000 18.89 0.04 44.11 3.46
493 497 1.526575 AAGCCCAACATGTGCTTCCG 61.527 55.000 14.35 0.00 41.23 4.30
494 498 2.568090 CCCAACATGTGCTTCCGC 59.432 61.111 0.00 0.00 0.00 5.54
495 499 2.176546 CCAACATGTGCTTCCGCG 59.823 61.111 0.00 0.00 39.65 6.46
496 500 2.324330 CCAACATGTGCTTCCGCGA 61.324 57.895 8.23 0.00 39.65 5.87
497 501 1.133253 CAACATGTGCTTCCGCGAG 59.867 57.895 8.23 0.00 39.65 5.03
498 502 1.005037 AACATGTGCTTCCGCGAGA 60.005 52.632 8.23 0.00 39.65 4.04
499 503 0.602638 AACATGTGCTTCCGCGAGAA 60.603 50.000 8.23 8.88 39.65 2.87
507 511 1.347320 CTTCCGCGAGAAGTACAACC 58.653 55.000 21.80 0.00 45.99 3.77
508 512 0.963962 TTCCGCGAGAAGTACAACCT 59.036 50.000 8.23 0.00 0.00 3.50
509 513 0.242825 TCCGCGAGAAGTACAACCTG 59.757 55.000 8.23 0.00 0.00 4.00
510 514 0.038526 CCGCGAGAAGTACAACCTGT 60.039 55.000 8.23 0.00 0.00 4.00
511 515 1.060713 CGCGAGAAGTACAACCTGTG 58.939 55.000 0.00 0.00 0.00 3.66
512 516 0.790814 GCGAGAAGTACAACCTGTGC 59.209 55.000 0.00 0.00 32.95 4.57
513 517 1.605712 GCGAGAAGTACAACCTGTGCT 60.606 52.381 0.00 0.00 45.19 4.40
520 524 4.085357 AGTACAACCTGTGCTTTCATGA 57.915 40.909 0.00 0.00 40.41 3.07
521 525 4.067896 AGTACAACCTGTGCTTTCATGAG 58.932 43.478 0.00 0.00 40.41 2.90
522 526 3.213206 ACAACCTGTGCTTTCATGAGA 57.787 42.857 0.00 0.00 0.00 3.27
523 527 2.880890 ACAACCTGTGCTTTCATGAGAC 59.119 45.455 0.00 0.00 0.00 3.36
524 528 1.800805 ACCTGTGCTTTCATGAGACG 58.199 50.000 0.00 0.00 0.00 4.18
525 529 1.070758 ACCTGTGCTTTCATGAGACGT 59.929 47.619 0.00 0.00 0.00 4.34
526 530 2.299013 ACCTGTGCTTTCATGAGACGTA 59.701 45.455 0.00 0.00 0.00 3.57
527 531 2.668457 CCTGTGCTTTCATGAGACGTAC 59.332 50.000 0.00 0.00 0.00 3.67
528 532 3.317150 CTGTGCTTTCATGAGACGTACA 58.683 45.455 0.00 3.92 0.00 2.90
529 533 3.723260 TGTGCTTTCATGAGACGTACAA 58.277 40.909 0.00 0.00 0.00 2.41
530 534 3.493129 TGTGCTTTCATGAGACGTACAAC 59.507 43.478 0.00 0.00 0.00 3.32
531 535 3.493129 GTGCTTTCATGAGACGTACAACA 59.507 43.478 0.00 0.00 0.00 3.33
532 536 4.152402 GTGCTTTCATGAGACGTACAACAT 59.848 41.667 0.00 0.00 0.00 2.71
533 537 4.152223 TGCTTTCATGAGACGTACAACATG 59.848 41.667 13.66 13.66 40.65 3.21
534 538 4.152402 GCTTTCATGAGACGTACAACATGT 59.848 41.667 16.98 0.00 40.32 3.21
535 539 5.590104 TTTCATGAGACGTACAACATGTG 57.410 39.130 0.00 0.00 40.32 3.21
536 540 4.251543 TCATGAGACGTACAACATGTGT 57.748 40.909 0.00 2.49 44.82 3.72
537 541 4.234574 TCATGAGACGTACAACATGTGTC 58.765 43.478 0.00 1.70 41.98 3.67
538 542 4.022329 TCATGAGACGTACAACATGTGTCT 60.022 41.667 13.85 13.85 41.98 3.41
539 543 4.316205 TGAGACGTACAACATGTGTCTT 57.684 40.909 14.81 2.40 41.98 3.01
549 553 6.698008 ACAACATGTGTCTTTCATGAGAAA 57.302 33.333 0.00 0.00 43.47 2.52
554 558 5.739752 TGTGTCTTTCATGAGAAACACAG 57.260 39.130 18.71 0.00 41.31 3.66
556 560 3.565482 TGTCTTTCATGAGAAACACAGCC 59.435 43.478 0.00 0.00 37.61 4.85
557 561 2.807967 TCTTTCATGAGAAACACAGCCG 59.192 45.455 0.00 0.00 38.76 5.52
576 580 0.889186 GTGCTCCCCGAAGAAAGCAA 60.889 55.000 0.00 0.00 45.55 3.91
579 583 2.290641 TGCTCCCCGAAGAAAGCAAATA 60.291 45.455 0.00 0.00 41.50 1.40
580 584 2.952310 GCTCCCCGAAGAAAGCAAATAT 59.048 45.455 0.00 0.00 34.86 1.28
598 602 6.310224 GCAAATATGCGCTTTTAGAAAAAGGA 59.690 34.615 9.73 0.75 43.83 3.36
599 603 7.148656 GCAAATATGCGCTTTTAGAAAAAGGAA 60.149 33.333 9.73 0.70 43.83 3.36
634 638 1.493311 CTTTCGCGAGAGGCACAAC 59.507 57.895 18.35 0.00 43.84 3.32
636 640 0.315886 TTTCGCGAGAGGCACAACTA 59.684 50.000 9.59 0.00 43.84 2.24
649 655 3.255642 GGCACAACTATGCTTCCTGAAAA 59.744 43.478 0.00 0.00 45.38 2.29
686 692 5.989551 ATGAAAAGCACAACCATGTTTTC 57.010 34.783 7.95 7.95 37.82 2.29
687 693 3.862267 TGAAAAGCACAACCATGTTTTCG 59.138 39.130 9.52 0.00 36.93 3.46
698 706 2.543430 CCATGTTTTCGTTTTTGGCCAG 59.457 45.455 5.11 0.00 0.00 4.85
735 743 8.773404 TTTTCCGGTTTTCATTTTTAGTTTCA 57.227 26.923 0.00 0.00 0.00 2.69
737 745 8.773404 TTCCGGTTTTCATTTTTAGTTTCAAA 57.227 26.923 0.00 0.00 0.00 2.69
738 746 8.187354 TCCGGTTTTCATTTTTAGTTTCAAAC 57.813 30.769 0.00 0.00 0.00 2.93
768 776 7.908827 TTGTTCTTTTGGTTTACCTTTTTCC 57.091 32.000 0.00 0.00 36.82 3.13
769 777 7.005709 TGTTCTTTTGGTTTACCTTTTTCCA 57.994 32.000 0.00 0.00 36.82 3.53
770 778 7.450903 TGTTCTTTTGGTTTACCTTTTTCCAA 58.549 30.769 0.00 0.00 36.55 3.53
771 779 8.103935 TGTTCTTTTGGTTTACCTTTTTCCAAT 58.896 29.630 0.00 0.00 37.87 3.16
772 780 8.952278 GTTCTTTTGGTTTACCTTTTTCCAATT 58.048 29.630 0.00 0.00 37.87 2.32
777 785 8.910351 TTGGTTTACCTTTTTCCAATTTATGG 57.090 30.769 0.00 0.00 43.25 2.74
778 786 7.454225 TGGTTTACCTTTTTCCAATTTATGGG 58.546 34.615 0.00 0.00 42.60 4.00
827 835 5.007234 CGCATCGAAACTTATTAACATGGGA 59.993 40.000 0.00 0.00 0.00 4.37
878 886 6.541111 AAGAGATTAGTGAAAACGGTTCAC 57.459 37.500 20.59 20.59 46.71 3.18
897 905 3.493129 TCACGATTTGAACGAGGACAAAG 59.507 43.478 0.00 0.00 38.94 2.77
903 911 1.149148 GAACGAGGACAAAGCTCCAC 58.851 55.000 0.00 0.00 31.94 4.02
992 1116 0.456221 TCCGGATTCGCTCTCACTTC 59.544 55.000 0.00 0.00 34.56 3.01
993 1117 0.528684 CCGGATTCGCTCTCACTTCC 60.529 60.000 0.00 0.00 34.56 3.46
996 1139 1.472376 GGATTCGCTCTCACTTCCCAG 60.472 57.143 0.00 0.00 0.00 4.45
1014 1157 2.644992 GAGCCGCACAAAGGTTGG 59.355 61.111 0.00 0.00 34.12 3.77
1015 1158 2.123897 AGCCGCACAAAGGTTGGT 60.124 55.556 0.00 0.00 34.12 3.67
1016 1159 0.887387 GAGCCGCACAAAGGTTGGTA 60.887 55.000 0.00 0.00 34.12 3.25
1054 1197 1.000993 GGAGAGAGAGTGGGGAGCA 59.999 63.158 0.00 0.00 0.00 4.26
1120 1263 0.252193 AGCTGCTCCACCTCTTCTCT 60.252 55.000 0.00 0.00 0.00 3.10
1153 1296 2.681778 ACCTCGCTCCCAGGTGAG 60.682 66.667 0.00 1.45 43.10 3.51
1155 1298 2.681778 CTCGCTCCCAGGTGAGGT 60.682 66.667 6.98 0.00 39.39 3.85
1156 1299 2.680352 TCGCTCCCAGGTGAGGTC 60.680 66.667 6.98 0.00 32.81 3.85
1157 1300 2.681778 CGCTCCCAGGTGAGGTCT 60.682 66.667 6.98 0.00 32.81 3.85
1158 1301 2.716017 CGCTCCCAGGTGAGGTCTC 61.716 68.421 6.98 0.00 32.81 3.36
1159 1302 2.363172 GCTCCCAGGTGAGGTCTCC 61.363 68.421 6.98 0.00 32.81 3.71
1160 1303 1.687493 CTCCCAGGTGAGGTCTCCC 60.687 68.421 0.00 0.00 0.00 4.30
1161 1304 2.122729 CCCAGGTGAGGTCTCCCA 59.877 66.667 7.77 0.00 0.00 4.37
1185 1328 1.052124 ATCCCATCCCGCCGACTTAA 61.052 55.000 0.00 0.00 0.00 1.85
1195 1338 2.943033 CCGCCGACTTAATTTCCTTCAT 59.057 45.455 0.00 0.00 0.00 2.57
1225 1368 1.608717 CCGTCACTCTCCTCCCCTTG 61.609 65.000 0.00 0.00 0.00 3.61
1232 1375 1.696884 CTCTCCTCCCCTTGCTAATCC 59.303 57.143 0.00 0.00 0.00 3.01
1246 1389 0.393808 TAATCCTGGTCTTTGCCGCC 60.394 55.000 0.00 0.00 0.00 6.13
1319 1462 3.594603 TGGACATCTTTCTCGGTTCTC 57.405 47.619 0.00 0.00 0.00 2.87
1327 1470 2.362632 CTCGGTTCTCTCCCCCGT 60.363 66.667 0.00 0.00 42.30 5.28
1389 1532 3.691118 GCAGATGCAGTTGAGGTGAATTA 59.309 43.478 0.00 0.00 41.59 1.40
1403 1546 2.930682 GTGAATTAACTCGGTCCTCTGC 59.069 50.000 0.00 0.00 0.00 4.26
1466 1618 8.880991 TGGATAGTACTTAGATAGATGGTTCC 57.119 38.462 0.00 0.00 0.00 3.62
1468 1620 7.611079 GGATAGTACTTAGATAGATGGTTCCGT 59.389 40.741 0.00 0.00 0.00 4.69
1469 1621 6.636562 AGTACTTAGATAGATGGTTCCGTG 57.363 41.667 0.00 0.00 0.00 4.94
1470 1622 6.127793 AGTACTTAGATAGATGGTTCCGTGT 58.872 40.000 0.00 0.00 0.00 4.49
1471 1623 5.263968 ACTTAGATAGATGGTTCCGTGTG 57.736 43.478 0.00 0.00 0.00 3.82
1472 1624 4.710375 ACTTAGATAGATGGTTCCGTGTGT 59.290 41.667 0.00 0.00 0.00 3.72
1473 1625 5.187186 ACTTAGATAGATGGTTCCGTGTGTT 59.813 40.000 0.00 0.00 0.00 3.32
1474 1626 4.124851 AGATAGATGGTTCCGTGTGTTC 57.875 45.455 0.00 0.00 0.00 3.18
1490 1642 1.980765 TGTTCTTCATGTGGAGCCTCT 59.019 47.619 0.00 0.00 0.00 3.69
1600 1752 3.435671 GGCATCGGTATATGTTGCTAACC 59.564 47.826 9.48 0.00 33.60 2.85
1639 1791 3.534554 CCTTTTCTGGTTTGCTTTGCTT 58.465 40.909 0.00 0.00 0.00 3.91
1764 1923 1.041447 ACGATTGGTACTCCCTCCGG 61.041 60.000 0.00 0.00 0.00 5.14
1776 1935 5.019657 ACTCCCTCCGGTCCATATTAATA 57.980 43.478 0.00 0.00 0.00 0.98
1777 1936 5.600749 ACTCCCTCCGGTCCATATTAATAT 58.399 41.667 0.00 1.91 0.00 1.28
1778 1937 5.425539 ACTCCCTCCGGTCCATATTAATATG 59.574 44.000 23.28 23.28 39.80 1.78
1952 2166 3.515502 ACAGTGAGTACATGTGCCATACT 59.484 43.478 9.11 8.87 31.79 2.12
1989 2203 1.475751 CCAATAGCCCACTGTAGCTGG 60.476 57.143 13.14 5.02 40.28 4.85
2114 2336 4.732285 ATACATGATGCCGATCGAAAAC 57.268 40.909 18.66 6.06 0.00 2.43
2296 2519 4.201812 CGCGAAGACATCACCATATGTTTT 60.202 41.667 0.00 0.00 40.17 2.43
2341 2564 5.999600 TCCAGGTGCATCATATTGTAATCTG 59.000 40.000 0.00 0.00 0.00 2.90
2347 2570 7.198390 GTGCATCATATTGTAATCTGCAGTTT 58.802 34.615 14.67 14.41 38.66 2.66
2350 2573 8.537223 GCATCATATTGTAATCTGCAGTTTTTG 58.463 33.333 14.67 3.75 0.00 2.44
2365 2588 5.609423 CAGTTTTTGGGAATCAATTCACCA 58.391 37.500 2.65 5.86 39.44 4.17
2378 2601 0.394762 TTCACCATCTGCCATGGAGC 60.395 55.000 18.40 0.45 41.64 4.70
2467 2696 5.583854 ACTTGTATGCTAAGTGAGATTGCTG 59.416 40.000 0.00 0.00 37.03 4.41
2503 2732 5.419542 TGTAGAAGGGTTCTGAATGAATCG 58.580 41.667 0.00 0.00 40.94 3.34
2539 2791 5.308014 ACTTGACATGACTTATGCTGACAA 58.692 37.500 0.00 0.00 40.59 3.18
2583 2835 5.258051 CCAGGTTTTGGTATTAGTTGCCTA 58.742 41.667 0.00 0.00 42.41 3.93
2658 2910 3.181476 ACCAATTTGTTGCCAAGTGAGAC 60.181 43.478 0.00 0.00 0.00 3.36
2663 2915 0.398318 GTTGCCAAGTGAGACCCTCT 59.602 55.000 0.00 0.00 0.00 3.69
2665 2917 2.024176 TGCCAAGTGAGACCCTCTTA 57.976 50.000 0.00 0.00 0.00 2.10
3049 3303 9.774742 GCTTTCTCATAGTATAAGTTTTTGTGG 57.225 33.333 0.00 0.00 0.00 4.17
3127 3381 0.109913 GGGGCCTAATAAACCCGGAG 59.890 60.000 0.73 0.00 45.27 4.63
3151 3410 5.195185 GGAGTAGTAGTTAAGAGACCTGCT 58.805 45.833 0.00 0.00 0.00 4.24
3247 3506 5.639506 CCCATAGCTTCATGTATTAGTTCCG 59.360 44.000 0.00 0.00 0.00 4.30
3403 3672 7.624549 TCAAGGAAAAGAGCTGTATCAGTTAT 58.375 34.615 0.00 0.00 33.43 1.89
3404 3673 8.103305 TCAAGGAAAAGAGCTGTATCAGTTATT 58.897 33.333 0.00 0.00 33.43 1.40
3405 3674 9.383519 CAAGGAAAAGAGCTGTATCAGTTATTA 57.616 33.333 0.00 0.00 33.43 0.98
3474 3753 2.776536 ACCTGCTCTCTGGCAAGAATAT 59.223 45.455 0.00 0.00 41.94 1.28
3477 3756 4.275443 CCTGCTCTCTGGCAAGAATATTTC 59.725 45.833 0.00 0.00 41.94 2.17
3511 3790 7.657761 ACAAACTTGACCTGAACTATTGTCTAG 59.342 37.037 0.00 0.00 36.88 2.43
3797 4084 6.754209 CCAATCTGTCATACTTGAGACTGTAC 59.246 42.308 0.00 0.00 35.83 2.90
3819 4106 3.536570 GTTCTCTATGCTTGTCCCCTTC 58.463 50.000 0.00 0.00 0.00 3.46
3842 4129 5.761234 TCCAGTAAAACATACACAACCAGAC 59.239 40.000 0.00 0.00 0.00 3.51
3853 4140 8.188139 ACATACACAACCAGACTTTTGTTTTAG 58.812 33.333 0.00 0.00 33.59 1.85
3936 4223 2.866028 CGCAAGCAGTTGGAGAGC 59.134 61.111 0.00 0.00 33.87 4.09
4050 4342 5.779241 TTTACATCCCATCCAGTCTTCTT 57.221 39.130 0.00 0.00 0.00 2.52
4065 4357 6.065374 CAGTCTTCTTCCTCTACTATAGCCA 58.935 44.000 0.00 0.00 0.00 4.75
4066 4358 6.719370 CAGTCTTCTTCCTCTACTATAGCCAT 59.281 42.308 0.00 0.00 0.00 4.40
4067 4359 7.885922 CAGTCTTCTTCCTCTACTATAGCCATA 59.114 40.741 0.00 0.00 0.00 2.74
4239 4656 8.814038 ATTAGCCTTGATGAAACATCTTTACT 57.186 30.769 11.98 7.73 0.00 2.24
4247 4664 9.725019 TTGATGAAACATCTTTACTAGTGTGAT 57.275 29.630 5.39 3.62 0.00 3.06
4254 4671 6.879458 ACATCTTTACTAGTGTGATTTGGACC 59.121 38.462 5.39 0.00 0.00 4.46
4262 4679 0.515564 GTGATTTGGACCGACAACCG 59.484 55.000 0.00 0.00 38.18 4.44
4281 4698 8.978953 ACAACCGTGTCAAAACATCCAGTTTG 62.979 42.308 0.00 0.00 41.01 2.93
4395 4814 7.495901 AGACGACTGAATATTGACAGAATGAT 58.504 34.615 10.31 0.00 39.69 2.45
4488 4907 4.128643 ACTTTGAATTGTGCCCAAACATG 58.871 39.130 0.00 0.00 33.44 3.21
4493 4912 4.525874 TGAATTGTGCCCAAACATGATACA 59.474 37.500 0.00 0.00 33.44 2.29
4537 4956 8.948631 AGGACACTGTATTCAATGTATTACAG 57.051 34.615 13.88 13.88 34.08 2.74
4565 4984 8.352137 TGAAAAATATGAACACATCTGACCAT 57.648 30.769 0.00 0.00 0.00 3.55
4610 5035 5.096849 GCAGAAGGTACGTTTTTGTTCAAA 58.903 37.500 1.77 0.00 0.00 2.69
4622 5047 7.061789 ACGTTTTTGTTCAAAGAATCAACAGAC 59.938 33.333 9.09 0.00 31.81 3.51
4623 5048 7.383361 GTTTTTGTTCAAAGAATCAACAGACG 58.617 34.615 0.00 0.00 31.81 4.18
4656 5081 7.209475 TGGCAAGTAAATTTTCTGGAAAAGAG 58.791 34.615 12.89 1.73 42.72 2.85
4680 5105 7.220030 AGTACACAAGATGAACAACTTCTCAT 58.780 34.615 0.00 0.00 34.96 2.90
4691 5116 5.108187 ACAACTTCTCATACATCAGGCAT 57.892 39.130 0.00 0.00 0.00 4.40
4713 5138 8.925161 GCATTAAGCCATTAAGTGATTTACAA 57.075 30.769 0.00 0.00 34.44 2.41
4728 5153 5.584251 TGATTTACAATCTGTCGCATTAGCA 59.416 36.000 0.00 0.00 42.27 3.49
4734 5173 2.826428 TCTGTCGCATTAGCAGGATTC 58.174 47.619 0.00 0.00 42.27 2.52
4739 5178 4.458989 TGTCGCATTAGCAGGATTCTTTTT 59.541 37.500 0.00 0.00 42.27 1.94
4767 5206 0.259065 TGAGGTCTCGCTGAGGGTAT 59.741 55.000 0.00 0.00 0.00 2.73
4791 5230 7.243604 TGAAATTATCAAAAATGCCCTGTCT 57.756 32.000 0.00 0.00 34.30 3.41
4794 5233 9.822185 GAAATTATCAAAAATGCCCTGTCTATT 57.178 29.630 0.00 0.00 0.00 1.73
4796 5235 5.603170 ATCAAAAATGCCCTGTCTATTGG 57.397 39.130 0.00 0.00 0.00 3.16
4813 5252 0.991920 TGGAGGCCTACCCTTTGAAG 59.008 55.000 14.06 0.00 46.60 3.02
4834 5273 2.686915 GGAACATGATTGCTTCTCCTGG 59.313 50.000 0.00 0.00 0.00 4.45
4842 5281 5.188434 TGATTGCTTCTCCTGGTCAATAAG 58.812 41.667 0.00 0.00 0.00 1.73
4883 5323 6.736794 GCAACATTTCAGAACAAACTCCAGAT 60.737 38.462 0.00 0.00 0.00 2.90
4884 5324 6.323203 ACATTTCAGAACAAACTCCAGATG 57.677 37.500 0.00 0.00 0.00 2.90
4893 5333 7.119699 CAGAACAAACTCCAGATGCAGTTAATA 59.880 37.037 0.00 0.00 32.36 0.98
4897 5337 8.637986 ACAAACTCCAGATGCAGTTAATAAAAA 58.362 29.630 0.00 0.00 32.36 1.94
4898 5338 8.915654 CAAACTCCAGATGCAGTTAATAAAAAC 58.084 33.333 0.00 0.00 32.36 2.43
4899 5339 7.759489 ACTCCAGATGCAGTTAATAAAAACA 57.241 32.000 0.00 0.00 0.00 2.83
4926 5366 0.833287 CATCTACTGTGGTCCCCTGG 59.167 60.000 0.00 0.00 0.00 4.45
4991 5431 7.667557 AGCTTCAGTACACTTGTCTTATGTTA 58.332 34.615 0.00 0.00 0.00 2.41
5105 5545 1.186200 CCTCTGTGAAGATCCGTGGA 58.814 55.000 0.00 0.00 0.00 4.02
5128 5568 6.550108 GGAACACCTGTAGAATAGAGACCATA 59.450 42.308 0.00 0.00 32.95 2.74
5160 5600 8.941995 TCTAGAAAGCTAGTGATACATGGTAT 57.058 34.615 0.00 0.00 43.72 2.73
5161 5601 9.368416 TCTAGAAAGCTAGTGATACATGGTATT 57.632 33.333 0.00 0.00 43.72 1.89
5235 5677 4.408182 ACTACCATGGAATCTTTCTCGG 57.592 45.455 21.47 0.00 0.00 4.63
5283 5725 1.238439 CACTTCGCAGGAACATTGGT 58.762 50.000 0.00 0.00 0.00 3.67
5301 5743 1.680249 GGTGTTGGAGCTTCATCCCTC 60.680 57.143 0.00 0.00 38.72 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.033194 GTGGCGTACAAGAGTGGGC 61.033 63.158 0.00 0.00 0.00 5.36
17 18 1.375523 GGGGTGGCGTACAAGAGTG 60.376 63.158 0.00 0.00 0.00 3.51
20 21 0.974010 CCTAGGGGTGGCGTACAAGA 60.974 60.000 0.00 0.00 0.00 3.02
46 48 1.852626 CCACCTTGGAGGAGGGGTT 60.853 63.158 0.07 0.00 41.76 4.11
76 78 2.293677 CCTCCACTATATATAGGCGCGG 59.706 54.545 21.20 15.53 34.69 6.46
79 81 3.068307 GCCACCTCCACTATATATAGGCG 59.932 52.174 21.20 12.75 34.69 5.52
129 133 1.210722 GAGGGAGGAGGCAACCTTTAG 59.789 57.143 4.85 0.00 40.73 1.85
156 160 5.107453 CGACAAGACAACTATTGTGGAAGAC 60.107 44.000 0.00 0.00 45.52 3.01
157 161 4.988540 CGACAAGACAACTATTGTGGAAGA 59.011 41.667 0.00 0.00 45.52 2.87
158 162 4.750098 ACGACAAGACAACTATTGTGGAAG 59.250 41.667 0.00 0.00 45.52 3.46
159 163 4.699637 ACGACAAGACAACTATTGTGGAA 58.300 39.130 0.00 0.00 45.52 3.53
190 194 4.296056 GGACCAACTAATTAGAGGGAGGA 58.704 47.826 24.31 0.00 0.00 3.71
194 198 4.037927 TCTGGGACCAACTAATTAGAGGG 58.962 47.826 19.38 19.20 0.00 4.30
355 359 6.713731 ATTCTACCAAAACCTAGGGAAAGA 57.286 37.500 14.81 3.17 0.00 2.52
356 360 7.670140 AGAAATTCTACCAAAACCTAGGGAAAG 59.330 37.037 14.81 0.00 0.00 2.62
374 378 6.183360 TGCTTCCCGAAAAGAAAAGAAATTCT 60.183 34.615 0.00 0.00 41.34 2.40
402 406 5.470098 ACAATTGTGCTTCTCGTAGAAATGT 59.530 36.000 11.07 0.00 33.19 2.71
421 425 6.323739 TCTTTCCCTTTTCAGTAAGCACAATT 59.676 34.615 0.00 0.00 0.00 2.32
431 435 4.236527 ACTGTGTCTTTCCCTTTTCAGT 57.763 40.909 0.00 0.00 0.00 3.41
464 468 5.118286 CACATGTTGGGCTTTTCTCTTTTT 58.882 37.500 0.00 0.00 0.00 1.94
491 495 0.038526 ACAGGTTGTACTTCTCGCGG 60.039 55.000 6.13 0.00 0.00 6.46
492 496 1.060713 CACAGGTTGTACTTCTCGCG 58.939 55.000 0.00 0.00 0.00 5.87
493 497 0.790814 GCACAGGTTGTACTTCTCGC 59.209 55.000 0.00 0.00 0.00 5.03
494 498 2.440539 AGCACAGGTTGTACTTCTCG 57.559 50.000 0.00 0.00 0.00 4.04
495 499 4.127171 TGAAAGCACAGGTTGTACTTCTC 58.873 43.478 0.00 0.00 33.11 2.87
496 500 4.150897 TGAAAGCACAGGTTGTACTTCT 57.849 40.909 0.00 0.00 33.11 2.85
497 501 4.515191 TCATGAAAGCACAGGTTGTACTTC 59.485 41.667 0.00 0.00 33.11 3.01
498 502 4.460263 TCATGAAAGCACAGGTTGTACTT 58.540 39.130 0.00 0.00 35.60 2.24
499 503 4.067896 CTCATGAAAGCACAGGTTGTACT 58.932 43.478 0.00 0.00 0.00 2.73
500 504 4.065088 TCTCATGAAAGCACAGGTTGTAC 58.935 43.478 0.00 0.00 0.00 2.90
501 505 4.065088 GTCTCATGAAAGCACAGGTTGTA 58.935 43.478 0.00 0.00 0.00 2.41
502 506 2.880890 GTCTCATGAAAGCACAGGTTGT 59.119 45.455 0.00 0.00 0.00 3.32
503 507 2.096069 CGTCTCATGAAAGCACAGGTTG 60.096 50.000 0.00 0.00 0.00 3.77
504 508 2.146342 CGTCTCATGAAAGCACAGGTT 58.854 47.619 0.00 0.00 0.00 3.50
505 509 1.070758 ACGTCTCATGAAAGCACAGGT 59.929 47.619 0.00 0.00 0.00 4.00
506 510 1.800805 ACGTCTCATGAAAGCACAGG 58.199 50.000 0.00 0.00 0.00 4.00
507 511 3.317150 TGTACGTCTCATGAAAGCACAG 58.683 45.455 0.00 0.00 0.00 3.66
508 512 3.378911 TGTACGTCTCATGAAAGCACA 57.621 42.857 0.00 0.00 0.00 4.57
509 513 3.493129 TGTTGTACGTCTCATGAAAGCAC 59.507 43.478 0.00 0.00 0.00 4.40
510 514 3.723260 TGTTGTACGTCTCATGAAAGCA 58.277 40.909 0.00 0.00 0.00 3.91
511 515 4.152402 ACATGTTGTACGTCTCATGAAAGC 59.848 41.667 20.56 0.00 39.68 3.51
512 516 5.177511 ACACATGTTGTACGTCTCATGAAAG 59.822 40.000 20.56 14.50 39.68 2.62
513 517 5.053811 ACACATGTTGTACGTCTCATGAAA 58.946 37.500 20.56 0.00 39.68 2.69
514 518 4.627058 ACACATGTTGTACGTCTCATGAA 58.373 39.130 20.56 2.74 39.68 2.57
515 519 4.022329 AGACACATGTTGTACGTCTCATGA 60.022 41.667 20.56 0.00 39.17 3.07
516 520 4.237724 AGACACATGTTGTACGTCTCATG 58.762 43.478 9.37 15.46 39.17 3.07
517 521 4.521130 AGACACATGTTGTACGTCTCAT 57.479 40.909 9.37 0.00 39.17 2.90
518 522 4.316205 AAGACACATGTTGTACGTCTCA 57.684 40.909 14.19 0.00 39.17 3.27
519 523 4.743151 TGAAAGACACATGTTGTACGTCTC 59.257 41.667 14.19 6.09 39.17 3.36
520 524 4.689071 TGAAAGACACATGTTGTACGTCT 58.311 39.130 9.37 9.37 39.17 4.18
521 525 5.176774 TCATGAAAGACACATGTTGTACGTC 59.823 40.000 0.00 0.00 43.56 4.34
522 526 5.053811 TCATGAAAGACACATGTTGTACGT 58.946 37.500 0.00 0.00 43.56 3.57
523 527 5.405269 TCTCATGAAAGACACATGTTGTACG 59.595 40.000 0.00 0.00 43.56 3.67
524 528 6.785488 TCTCATGAAAGACACATGTTGTAC 57.215 37.500 0.00 0.00 43.56 2.90
525 529 7.281999 TGTTTCTCATGAAAGACACATGTTGTA 59.718 33.333 0.00 0.00 42.15 2.41
526 530 6.095300 TGTTTCTCATGAAAGACACATGTTGT 59.905 34.615 0.00 0.00 42.15 3.32
527 531 6.497437 TGTTTCTCATGAAAGACACATGTTG 58.503 36.000 0.00 0.00 42.15 3.33
528 532 6.698008 TGTTTCTCATGAAAGACACATGTT 57.302 33.333 0.00 0.00 42.15 2.71
536 540 2.807967 CGGCTGTGTTTCTCATGAAAGA 59.192 45.455 0.00 0.00 42.15 2.52
537 541 2.549754 ACGGCTGTGTTTCTCATGAAAG 59.450 45.455 0.00 0.00 42.15 2.62
538 542 2.290367 CACGGCTGTGTTTCTCATGAAA 59.710 45.455 17.96 0.00 41.34 2.69
539 543 1.872952 CACGGCTGTGTTTCTCATGAA 59.127 47.619 17.96 0.00 41.34 2.57
554 558 3.894547 TTTCTTCGGGGAGCACGGC 62.895 63.158 0.00 0.00 0.00 5.68
556 560 2.391389 GCTTTCTTCGGGGAGCACG 61.391 63.158 0.00 0.00 35.29 5.34
557 561 0.889186 TTGCTTTCTTCGGGGAGCAC 60.889 55.000 0.00 0.00 44.07 4.40
562 566 3.084070 GCATATTTGCTTTCTTCGGGG 57.916 47.619 0.35 0.00 45.77 5.73
576 580 8.825667 TTTTCCTTTTTCTAAAAGCGCATATT 57.174 26.923 11.47 3.61 0.00 1.28
620 624 1.756375 GCATAGTTGTGCCTCTCGCG 61.756 60.000 0.00 0.00 42.08 5.87
621 625 0.460987 AGCATAGTTGTGCCTCTCGC 60.461 55.000 0.00 0.00 46.19 5.03
686 692 2.301577 TCCAAAACTGGCCAAAAACG 57.698 45.000 7.01 0.00 0.00 3.60
687 693 4.071961 AGATCCAAAACTGGCCAAAAAC 57.928 40.909 7.01 0.00 0.00 2.43
709 717 9.216117 TGAAACTAAAAATGAAAACCGGAAAAA 57.784 25.926 9.46 0.00 0.00 1.94
714 722 8.192068 AGTTTGAAACTAAAAATGAAAACCGG 57.808 30.769 9.13 0.00 40.69 5.28
744 752 7.450903 TGGAAAAAGGTAAACCAAAAGAACAA 58.549 30.769 1.26 0.00 38.89 2.83
745 753 7.005709 TGGAAAAAGGTAAACCAAAAGAACA 57.994 32.000 1.26 0.00 38.89 3.18
782 790 7.531280 TGCGTCTTTTTCATGAAAAATCAAA 57.469 28.000 34.76 22.21 45.69 2.69
785 793 6.305399 TCGATGCGTCTTTTTCATGAAAAATC 59.695 34.615 34.76 27.69 45.69 2.17
786 794 6.148948 TCGATGCGTCTTTTTCATGAAAAAT 58.851 32.000 34.76 23.92 45.69 1.82
789 797 4.740741 TCGATGCGTCTTTTTCATGAAA 57.259 36.364 16.91 16.91 0.00 2.69
790 798 4.740741 TTCGATGCGTCTTTTTCATGAA 57.259 36.364 3.38 3.38 0.00 2.57
791 799 4.213270 AGTTTCGATGCGTCTTTTTCATGA 59.787 37.500 4.05 0.00 0.00 3.07
793 801 4.749245 AGTTTCGATGCGTCTTTTTCAT 57.251 36.364 4.05 0.00 0.00 2.57
794 802 4.545823 AAGTTTCGATGCGTCTTTTTCA 57.454 36.364 4.05 0.00 0.00 2.69
795 803 8.564766 GTTAATAAGTTTCGATGCGTCTTTTTC 58.435 33.333 4.05 0.00 0.00 2.29
796 804 8.071368 TGTTAATAAGTTTCGATGCGTCTTTTT 58.929 29.630 4.05 0.00 0.00 1.94
802 810 5.220777 CCCATGTTAATAAGTTTCGATGCGT 60.221 40.000 0.00 0.00 0.00 5.24
846 854 8.861101 CGTTTTCACTAATCTCTTTCTCGTATT 58.139 33.333 0.00 0.00 0.00 1.89
855 863 5.176958 CGTGAACCGTTTTCACTAATCTCTT 59.823 40.000 19.38 0.00 44.79 2.85
859 867 4.977741 TCGTGAACCGTTTTCACTAATC 57.022 40.909 19.38 0.60 44.79 1.75
861 869 5.293814 TCAAATCGTGAACCGTTTTCACTAA 59.706 36.000 19.38 11.25 44.79 2.24
864 872 3.942739 TCAAATCGTGAACCGTTTTCAC 58.057 40.909 14.31 14.31 43.85 3.18
878 886 2.480419 AGCTTTGTCCTCGTTCAAATCG 59.520 45.455 0.00 0.00 33.93 3.34
903 911 1.202463 CGCTCTGAGTCCCACCTTATG 60.202 57.143 6.53 0.00 0.00 1.90
992 1116 3.058160 CTTTGTGCGGCTCCTGGG 61.058 66.667 0.00 0.00 0.00 4.45
993 1117 3.058160 CCTTTGTGCGGCTCCTGG 61.058 66.667 0.00 0.00 0.00 4.45
996 1139 2.644992 CAACCTTTGTGCGGCTCC 59.355 61.111 0.00 0.00 0.00 4.70
1014 1157 2.101582 TCGACTCCTACGGTCCTACTAC 59.898 54.545 0.00 0.00 0.00 2.73
1015 1158 2.363680 CTCGACTCCTACGGTCCTACTA 59.636 54.545 0.00 0.00 0.00 1.82
1016 1159 1.138661 CTCGACTCCTACGGTCCTACT 59.861 57.143 0.00 0.00 0.00 2.57
1031 1174 0.750182 CCCCACTCTCTCTCCTCGAC 60.750 65.000 0.00 0.00 0.00 4.20
1120 1263 0.251832 AGGTGAGGAAGGAGAAGCGA 60.252 55.000 0.00 0.00 0.00 4.93
1154 1297 0.695347 GATGGGATGGGATGGGAGAC 59.305 60.000 0.00 0.00 0.00 3.36
1155 1298 0.476415 GGATGGGATGGGATGGGAGA 60.476 60.000 0.00 0.00 0.00 3.71
1156 1299 1.504275 GGGATGGGATGGGATGGGAG 61.504 65.000 0.00 0.00 0.00 4.30
1157 1300 1.465986 GGGATGGGATGGGATGGGA 60.466 63.158 0.00 0.00 0.00 4.37
1158 1301 2.910737 CGGGATGGGATGGGATGGG 61.911 68.421 0.00 0.00 0.00 4.00
1159 1302 2.759114 CGGGATGGGATGGGATGG 59.241 66.667 0.00 0.00 0.00 3.51
1160 1303 2.034687 GCGGGATGGGATGGGATG 59.965 66.667 0.00 0.00 0.00 3.51
1161 1304 3.260100 GGCGGGATGGGATGGGAT 61.260 66.667 0.00 0.00 0.00 3.85
1185 1328 3.117360 GGGGGATCAGTGATGAAGGAAAT 60.117 47.826 11.20 0.00 0.00 2.17
1195 1338 0.970937 GAGTGACGGGGGATCAGTGA 60.971 60.000 0.00 0.00 29.66 3.41
1225 1368 1.017387 CGGCAAAGACCAGGATTAGC 58.983 55.000 0.00 0.00 0.00 3.09
1232 1375 3.121030 CTCGGCGGCAAAGACCAG 61.121 66.667 10.53 0.00 0.00 4.00
1246 1389 2.610727 GGTCCTTGAACTCTGGAACTCG 60.611 54.545 0.00 0.00 34.90 4.18
1319 1462 0.546598 AGCAAAGGAATACGGGGGAG 59.453 55.000 0.00 0.00 0.00 4.30
1346 1489 6.758416 TCTGCACAAATTACAGATGCTACTAG 59.242 38.462 0.00 0.00 35.58 2.57
1376 1519 3.683340 GGACCGAGTTAATTCACCTCAAC 59.317 47.826 0.00 0.00 0.00 3.18
1381 1524 3.522553 CAGAGGACCGAGTTAATTCACC 58.477 50.000 0.00 0.00 0.00 4.02
1389 1532 0.759346 AAACTGCAGAGGACCGAGTT 59.241 50.000 23.35 0.00 0.00 3.01
1403 1546 5.066375 TCACTGTCCAAACTGAATGAAACTG 59.934 40.000 0.00 0.00 0.00 3.16
1465 1617 1.800586 CTCCACATGAAGAACACACGG 59.199 52.381 0.00 0.00 0.00 4.94
1466 1618 1.195448 GCTCCACATGAAGAACACACG 59.805 52.381 0.00 0.00 0.00 4.49
1468 1620 1.421268 AGGCTCCACATGAAGAACACA 59.579 47.619 0.00 0.00 0.00 3.72
1469 1621 2.079925 GAGGCTCCACATGAAGAACAC 58.920 52.381 2.15 0.00 0.00 3.32
1470 1622 1.980765 AGAGGCTCCACATGAAGAACA 59.019 47.619 11.71 0.00 0.00 3.18
1471 1623 2.235898 AGAGAGGCTCCACATGAAGAAC 59.764 50.000 11.71 0.00 0.00 3.01
1472 1624 2.499289 GAGAGAGGCTCCACATGAAGAA 59.501 50.000 11.71 0.00 37.69 2.52
1473 1625 2.106566 GAGAGAGGCTCCACATGAAGA 58.893 52.381 11.71 0.00 37.69 2.87
1474 1626 2.109774 AGAGAGAGGCTCCACATGAAG 58.890 52.381 11.71 0.00 45.10 3.02
1547 1699 0.467804 GGATCTCTTCCTGCACCTCC 59.532 60.000 0.00 0.00 41.78 4.30
1556 1708 1.025812 TCTCGCGAAGGATCTCTTCC 58.974 55.000 11.33 8.97 46.93 3.46
1559 1711 0.958091 CCATCTCGCGAAGGATCTCT 59.042 55.000 11.33 0.00 29.43 3.10
1600 1752 1.065273 GCATGGAGCCAAGAATGCG 59.935 57.895 0.00 0.00 36.41 4.73
1639 1791 2.004733 CATCTGCACAAGAATCGCTGA 58.995 47.619 0.00 0.00 38.79 4.26
1776 1935 0.031716 TGCTACTCCCTCTGCTCCAT 60.032 55.000 0.00 0.00 0.00 3.41
1777 1936 0.031716 ATGCTACTCCCTCTGCTCCA 60.032 55.000 0.00 0.00 0.00 3.86
1778 1937 2.002505 TATGCTACTCCCTCTGCTCC 57.997 55.000 0.00 0.00 0.00 4.70
1779 1938 4.202305 ACAAATATGCTACTCCCTCTGCTC 60.202 45.833 0.00 0.00 0.00 4.26
1780 1939 3.713764 ACAAATATGCTACTCCCTCTGCT 59.286 43.478 0.00 0.00 0.00 4.24
1781 1940 4.078639 ACAAATATGCTACTCCCTCTGC 57.921 45.455 0.00 0.00 0.00 4.26
1782 1941 6.203723 GCTTTACAAATATGCTACTCCCTCTG 59.796 42.308 0.00 0.00 0.00 3.35
1783 1942 6.100424 AGCTTTACAAATATGCTACTCCCTCT 59.900 38.462 0.00 0.00 31.71 3.69
1890 2104 4.846940 ACAGGAAGTATGGACCTCTTCTTT 59.153 41.667 17.38 8.90 38.02 2.52
1952 2166 5.646360 GCTATTGGCTAAACAGTAACTCCAA 59.354 40.000 0.00 0.00 38.06 3.53
2168 2390 5.104485 AGTTTTCTACCAGACCAAACTCACT 60.104 40.000 1.82 0.00 32.68 3.41
2296 2519 6.880484 TGGACACAACTGAAGTAGAAACTAA 58.120 36.000 0.00 0.00 33.75 2.24
2341 2564 4.452114 GGTGAATTGATTCCCAAAAACTGC 59.548 41.667 1.56 0.00 38.43 4.40
2347 2570 4.081531 GCAGATGGTGAATTGATTCCCAAA 60.082 41.667 13.97 0.00 39.14 3.28
2350 2573 2.363359 GGCAGATGGTGAATTGATTCCC 59.637 50.000 1.56 3.56 35.97 3.97
2365 2588 1.229359 CAAGGGCTCCATGGCAGAT 59.771 57.895 6.96 0.00 43.83 2.90
2503 2732 5.456822 GTCATGTCAAGTCAAAGAAAAGCAC 59.543 40.000 0.00 0.00 0.00 4.40
2583 2835 2.930826 ACATGACGTTCACCTTTCCT 57.069 45.000 0.00 0.00 0.00 3.36
2599 2851 8.793592 CATCAAATCCATGTCATTCTCATACAT 58.206 33.333 0.00 0.00 34.22 2.29
3077 3331 8.831715 ATTTTGGCCTAAAGTTTGACAATAAG 57.168 30.769 17.29 0.00 0.00 1.73
3095 3349 0.032117 AGGCCCCCTCTTATTTTGGC 60.032 55.000 0.00 0.00 38.16 4.52
3127 3381 4.338964 GCAGGTCTCTTAACTACTACTCCC 59.661 50.000 0.00 0.00 0.00 4.30
3133 3387 7.201839 GCATTACTAGCAGGTCTCTTAACTACT 60.202 40.741 0.00 0.00 0.00 2.57
3134 3388 6.919115 GCATTACTAGCAGGTCTCTTAACTAC 59.081 42.308 0.00 0.00 0.00 2.73
3135 3389 6.834451 AGCATTACTAGCAGGTCTCTTAACTA 59.166 38.462 0.00 0.00 0.00 2.24
3136 3390 5.659079 AGCATTACTAGCAGGTCTCTTAACT 59.341 40.000 0.00 0.00 0.00 2.24
3137 3391 5.908341 AGCATTACTAGCAGGTCTCTTAAC 58.092 41.667 0.00 0.00 0.00 2.01
3138 3392 6.546428 AAGCATTACTAGCAGGTCTCTTAA 57.454 37.500 0.00 0.00 0.00 1.85
3230 3489 6.037062 TGCAACATCGGAACTAATACATGAAG 59.963 38.462 0.00 0.00 0.00 3.02
3247 3506 3.806625 ATGTAAAGGCCATGCAACATC 57.193 42.857 5.01 0.00 0.00 3.06
3297 3564 9.509956 AACTTGCACTACCATATAAGTTGTTTA 57.490 29.630 0.00 0.00 37.09 2.01
3403 3672 2.493675 TGTTTTATGGCTGGCGCATTAA 59.506 40.909 10.83 0.00 38.10 1.40
3404 3673 2.095461 TGTTTTATGGCTGGCGCATTA 58.905 42.857 10.83 0.00 38.10 1.90
3405 3674 0.894141 TGTTTTATGGCTGGCGCATT 59.106 45.000 10.83 0.00 38.10 3.56
3474 3753 4.701171 AGGTCAAGTTTGTAAACCACGAAA 59.299 37.500 4.00 0.00 39.71 3.46
3477 3756 3.623960 TCAGGTCAAGTTTGTAAACCACG 59.376 43.478 4.00 0.00 39.71 4.94
3511 3790 5.221322 GGGGAAATAATCAGAACATGGCTTC 60.221 44.000 0.00 0.00 0.00 3.86
3797 4084 1.482593 AGGGGACAAGCATAGAGAACG 59.517 52.381 0.00 0.00 0.00 3.95
3819 4106 5.763204 AGTCTGGTTGTGTATGTTTTACTGG 59.237 40.000 0.00 0.00 0.00 4.00
3936 4223 2.537529 CGCACTGGTATCAAAATCAGCG 60.538 50.000 0.00 0.00 35.42 5.18
4050 4342 5.522315 AGCTGTATGGCTATAGTAGAGGA 57.478 43.478 0.84 0.00 41.16 3.71
4065 4357 7.770433 TGCAGATTACATGAAGTAAAGCTGTAT 59.230 33.333 0.00 0.00 45.25 2.29
4066 4358 7.064609 GTGCAGATTACATGAAGTAAAGCTGTA 59.935 37.037 0.00 11.84 45.25 2.74
4067 4359 5.939883 TGCAGATTACATGAAGTAAAGCTGT 59.060 36.000 0.00 0.00 45.25 4.40
4228 4645 7.390718 GGTCCAAATCACACTAGTAAAGATGTT 59.609 37.037 0.00 0.00 0.00 2.71
4236 4653 3.827876 TGTCGGTCCAAATCACACTAGTA 59.172 43.478 0.00 0.00 0.00 1.82
4239 4656 3.395639 GTTGTCGGTCCAAATCACACTA 58.604 45.455 0.00 0.00 0.00 2.74
4247 4664 0.810823 GACACGGTTGTCGGTCCAAA 60.811 55.000 0.00 0.00 42.86 3.28
4262 4679 4.044426 GCTCAAACTGGATGTTTTGACAC 58.956 43.478 0.00 0.00 45.69 3.67
4395 4814 5.906495 TGTTGGCCCTTAGTATTACCATAGA 59.094 40.000 0.00 0.00 0.00 1.98
4405 4824 3.649023 TCTTCTTGTGTTGGCCCTTAGTA 59.351 43.478 0.00 0.00 0.00 1.82
4412 4831 5.391312 AATGTAATCTTCTTGTGTTGGCC 57.609 39.130 0.00 0.00 0.00 5.36
4441 4860 2.611722 GGAGAACAGGAGAAGTCAGCAC 60.612 54.545 0.00 0.00 0.00 4.40
4493 4912 8.986991 AGTGTCCTATCAAAGATAGAAATGTCT 58.013 33.333 14.03 0.00 37.95 3.41
4532 4951 7.517614 TGTGTTCATATTTTTCAGCCTGTAA 57.482 32.000 0.00 0.00 0.00 2.41
4537 4956 6.749118 GTCAGATGTGTTCATATTTTTCAGCC 59.251 38.462 0.00 0.00 34.06 4.85
4565 4984 3.485394 TGTGCAGATGGACAAGCTAAAA 58.515 40.909 4.56 0.00 43.38 1.52
4610 5035 4.382470 CCAAGATCTCCGTCTGTTGATTCT 60.382 45.833 0.00 0.00 0.00 2.40
4622 5047 5.567138 AAATTTACTTGCCAAGATCTCCG 57.433 39.130 12.25 0.00 0.00 4.63
4623 5048 7.031975 CAGAAAATTTACTTGCCAAGATCTCC 58.968 38.462 12.25 0.00 0.00 3.71
4656 5081 6.844696 TGAGAAGTTGTTCATCTTGTGTAC 57.155 37.500 1.55 0.00 34.82 2.90
4660 5085 7.879677 TGATGTATGAGAAGTTGTTCATCTTGT 59.120 33.333 3.40 0.00 35.72 3.16
4713 5138 3.070734 AGAATCCTGCTAATGCGACAGAT 59.929 43.478 0.00 0.00 43.34 2.90
4717 5142 4.622701 AAAAGAATCCTGCTAATGCGAC 57.377 40.909 0.00 0.00 43.34 5.19
4728 5153 9.620259 GACCTCAGTTATCATAAAAAGAATCCT 57.380 33.333 0.00 0.00 0.00 3.24
4734 5173 6.758886 AGCGAGACCTCAGTTATCATAAAAAG 59.241 38.462 0.00 0.00 0.00 2.27
4739 5178 4.461198 TCAGCGAGACCTCAGTTATCATA 58.539 43.478 0.00 0.00 0.00 2.15
4750 5189 0.259065 TCATACCCTCAGCGAGACCT 59.741 55.000 7.07 0.00 0.00 3.85
4756 5195 6.618287 TTTGATAATTTCATACCCTCAGCG 57.382 37.500 0.00 0.00 33.34 5.18
4767 5206 7.243604 AGACAGGGCATTTTTGATAATTTCA 57.756 32.000 0.00 0.00 0.00 2.69
4791 5230 2.853430 TCAAAGGGTAGGCCTCCAATA 58.147 47.619 9.68 0.00 34.45 1.90
4794 5233 0.991920 CTTCAAAGGGTAGGCCTCCA 59.008 55.000 9.68 0.00 34.45 3.86
4796 5235 1.286248 TCCTTCAAAGGGTAGGCCTC 58.714 55.000 9.68 0.00 46.47 4.70
4813 5252 2.686915 CCAGGAGAAGCAATCATGTTCC 59.313 50.000 0.00 0.00 0.00 3.62
4817 5256 2.995283 TGACCAGGAGAAGCAATCATG 58.005 47.619 0.00 0.00 0.00 3.07
4822 5261 4.640771 ACTTATTGACCAGGAGAAGCAA 57.359 40.909 0.00 0.00 0.00 3.91
4834 5273 6.258947 GCTGGAAGATGAGGTAACTTATTGAC 59.741 42.308 0.00 0.00 44.07 3.18
4842 5281 3.674997 TGTTGCTGGAAGATGAGGTAAC 58.325 45.455 0.00 0.00 34.07 2.50
4883 5323 8.201554 TGTGCAATTTGTTTTTATTAACTGCA 57.798 26.923 0.00 0.00 34.87 4.41
4884 5324 9.316859 GATGTGCAATTTGTTTTTATTAACTGC 57.683 29.630 0.00 0.00 0.00 4.40
5018 5458 4.422073 TGATGACCGCTTTATCTTGGAT 57.578 40.909 0.00 0.00 0.00 3.41
5024 5464 5.233225 TCTGATGATGATGACCGCTTTATC 58.767 41.667 0.00 0.00 0.00 1.75
5105 5545 7.620094 ACTTATGGTCTCTATTCTACAGGTGTT 59.380 37.037 0.00 0.00 0.00 3.32
5215 5657 3.733337 CCCGAGAAAGATTCCATGGTAG 58.267 50.000 12.58 0.00 0.00 3.18
5226 5668 1.537889 TGGGGAAGCCCGAGAAAGA 60.538 57.895 0.00 0.00 46.66 2.52
5252 5694 4.100963 TCCTGCGAAGTGGTGATATTGTAT 59.899 41.667 0.00 0.00 0.00 2.29
5283 5725 0.250234 CGAGGGATGAAGCTCCAACA 59.750 55.000 0.00 0.00 37.01 3.33


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

AutoCloner maintained by Alex Coulton.