Multiple sequence alignment - TraesCS1A01G077600

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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 TraesCS1A01G077600 chr1A 100.000 5899 0 0 1 5899 60359841 60353943 0.000000e+00 10894.0
1 TraesCS1A01G077600 chr1D 95.575 3571 129 14 836 4387 62419792 62416232 0.000000e+00 5692.0
2 TraesCS1A01G077600 chr1D 88.594 754 33 19 5132 5856 62415523 62414794 0.000000e+00 867.0
3 TraesCS1A01G077600 chr1D 89.740 692 40 15 4467 5139 62416232 62415553 0.000000e+00 856.0
4 TraesCS1A01G077600 chr1D 88.921 343 33 3 18 359 478693772 478694110 9.140000e-113 418.0
5 TraesCS1A01G077600 chr1B 94.584 3619 162 21 791 4387 99600016 99596410 0.000000e+00 5566.0
6 TraesCS1A01G077600 chr1B 91.520 684 38 8 4467 5139 99596410 99595736 0.000000e+00 924.0
7 TraesCS1A01G077600 chr1B 87.420 779 39 18 5132 5892 99595705 99594968 0.000000e+00 841.0
8 TraesCS1A01G077600 chr1B 86.316 95 8 2 4385 4475 439444813 439444720 1.350000e-16 99.0
9 TraesCS1A01G077600 chr3A 94.236 399 23 0 128 526 714512377 714511979 1.410000e-170 610.0
10 TraesCS1A01G077600 chr3A 90.378 291 27 1 500 790 714511945 714511656 1.200000e-101 381.0
11 TraesCS1A01G077600 chr3A 95.349 43 2 0 484 526 714511875 714511833 1.060000e-07 69.4
12 TraesCS1A01G077600 chr6A 87.765 425 44 7 113 534 35156676 35156257 1.910000e-134 490.0
13 TraesCS1A01G077600 chr6A 86.735 98 7 3 4383 4475 604890662 604890758 2.910000e-18 104.0
14 TraesCS1A01G077600 chr3D 91.011 267 22 2 268 534 574742281 574742017 5.620000e-95 359.0
15 TraesCS1A01G077600 chr3D 91.667 84 3 1 4386 4465 131489253 131489170 4.830000e-21 113.0
16 TraesCS1A01G077600 chr3D 87.368 95 7 2 4386 4475 389633215 389633121 2.910000e-18 104.0
17 TraesCS1A01G077600 chr5B 77.338 631 115 22 3 612 537901333 537901956 1.220000e-91 348.0
18 TraesCS1A01G077600 chr7B 80.769 468 69 14 162 612 566619076 566618613 4.380000e-91 346.0
19 TraesCS1A01G077600 chr7B 78.351 388 54 14 248 612 48778361 48778741 2.140000e-54 224.0
20 TraesCS1A01G077600 chr7B 89.412 85 5 2 4385 4465 482484950 482485034 2.910000e-18 104.0
21 TraesCS1A01G077600 chr4D 88.298 94 6 2 4386 4474 107696609 107696516 2.250000e-19 108.0
22 TraesCS1A01G077600 chr5D 89.412 85 5 1 4389 4469 530069374 530069290 2.910000e-18 104.0
23 TraesCS1A01G077600 chr7A 88.372 86 9 1 4386 4471 474730880 474730796 1.050000e-17 102.0
24 TraesCS1A01G077600 chr2A 86.957 92 9 2 4386 4474 632593210 632593119 3.760000e-17 100.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G077600 chr1A 60353943 60359841 5898 True 10894.000000 10894 100.000000 1 5899 1 chr1A.!!$R1 5898
1 TraesCS1A01G077600 chr1D 62414794 62419792 4998 True 2471.666667 5692 91.303000 836 5856 3 chr1D.!!$R1 5020
2 TraesCS1A01G077600 chr1B 99594968 99600016 5048 True 2443.666667 5566 91.174667 791 5892 3 chr1B.!!$R2 5101
3 TraesCS1A01G077600 chr3A 714511656 714512377 721 True 353.466667 610 93.321000 128 790 3 chr3A.!!$R1 662
4 TraesCS1A01G077600 chr5B 537901333 537901956 623 False 348.000000 348 77.338000 3 612 1 chr5B.!!$F1 609

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
97 98 0.032678 CCTACTACCATGGCTCGCAG 59.967 60.000 13.04 4.03 0.0 5.18 F
1701 1789 0.040942 CCCACCATCACCCCATTCAA 59.959 55.000 0.00 0.00 0.0 2.69 F
1809 1897 0.768622 ATTGGTTGACGGGAGGACAA 59.231 50.000 0.00 0.00 0.0 3.18 F
2507 2609 0.108281 GCTGTCCGGGAGTAAGAACC 60.108 60.000 0.00 0.00 0.0 3.62 F
2529 2631 0.613012 AATTCTGGGGCTGCTGTTCC 60.613 55.000 0.00 0.00 0.0 3.62 F
4319 4429 1.202976 ACTTGGAACCTCTGCTGCATT 60.203 47.619 1.31 0.00 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 1929 0.178992 CTCCCAGCACCCAAAGACAA 60.179 55.0 0.00 0.0 0.00 3.18 R
2507 2609 0.323178 ACAGCAGCCCCAGAATTCAG 60.323 55.0 8.44 0.0 0.00 3.02 R
2833 2938 0.583438 CATGGCGATTACTTCCAGCG 59.417 55.0 0.00 0.0 32.78 5.18 R
4451 4563 0.032515 TAGTTGCTCCCTCCGATCCA 60.033 55.0 0.00 0.0 0.00 3.41 R
4476 4588 0.252479 ATGGCTCTGCAAGTGAGGAG 59.748 55.0 3.87 0.0 33.76 3.69 R
5658 5858 0.250513 CTCACCTAACCCACAGCTCC 59.749 60.0 0.00 0.0 0.00 4.70 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
35 36 5.567623 CGATGGCCTTATAATGCTACTCTGT 60.568 44.000 3.32 0.00 0.00 3.41
36 37 5.630415 TGGCCTTATAATGCTACTCTGTT 57.370 39.130 3.32 0.00 0.00 3.16
37 38 6.001449 TGGCCTTATAATGCTACTCTGTTT 57.999 37.500 3.32 0.00 0.00 2.83
45 46 2.479837 TGCTACTCTGTTTCAACACCG 58.520 47.619 0.00 0.00 34.70 4.94
46 47 1.194772 GCTACTCTGTTTCAACACCGC 59.805 52.381 0.00 0.00 34.70 5.68
84 85 0.035439 GCAAAGCAGCCACCCTACTA 60.035 55.000 0.00 0.00 0.00 1.82
86 87 0.618981 AAAGCAGCCACCCTACTACC 59.381 55.000 0.00 0.00 0.00 3.18
87 88 0.546747 AAGCAGCCACCCTACTACCA 60.547 55.000 0.00 0.00 0.00 3.25
88 89 0.326618 AGCAGCCACCCTACTACCAT 60.327 55.000 0.00 0.00 0.00 3.55
89 90 0.179045 GCAGCCACCCTACTACCATG 60.179 60.000 0.00 0.00 0.00 3.66
90 91 0.469917 CAGCCACCCTACTACCATGG 59.530 60.000 11.19 11.19 0.00 3.66
92 93 2.930935 CCACCCTACTACCATGGCT 58.069 57.895 13.04 1.45 0.00 4.75
93 94 0.759346 CCACCCTACTACCATGGCTC 59.241 60.000 13.04 0.00 0.00 4.70
94 95 0.389391 CACCCTACTACCATGGCTCG 59.611 60.000 13.04 2.49 0.00 5.03
95 96 1.367840 CCCTACTACCATGGCTCGC 59.632 63.158 13.04 0.00 0.00 5.03
96 97 1.399744 CCCTACTACCATGGCTCGCA 61.400 60.000 13.04 0.00 0.00 5.10
97 98 0.032678 CCTACTACCATGGCTCGCAG 59.967 60.000 13.04 4.03 0.00 5.18
98 99 0.032678 CTACTACCATGGCTCGCAGG 59.967 60.000 13.04 0.00 0.00 4.85
99 100 0.396556 TACTACCATGGCTCGCAGGA 60.397 55.000 13.04 0.00 0.00 3.86
101 102 1.680522 CTACCATGGCTCGCAGGAGT 61.681 60.000 13.04 0.00 42.53 3.85
106 107 4.742201 GGCTCGCAGGAGTCGCAA 62.742 66.667 0.00 0.00 42.53 4.85
117 120 1.571919 GAGTCGCAACCGCTATTGAT 58.428 50.000 1.27 0.00 35.30 2.57
139 143 0.104304 AAGCAACGAAGGTCGACACT 59.896 50.000 18.91 9.30 43.74 3.55
146 150 1.557443 GAAGGTCGACACTGGCAACG 61.557 60.000 18.91 0.00 42.51 4.10
152 157 1.372499 GACACTGGCAACGCTACGA 60.372 57.895 0.00 0.00 42.51 3.43
154 159 1.663388 CACTGGCAACGCTACGACA 60.663 57.895 0.00 0.00 42.51 4.35
231 236 4.314440 TCGCCACTGCCACTCCAC 62.314 66.667 0.00 0.00 0.00 4.02
256 262 2.070783 CAATCCATGTGTTTTGCAGCC 58.929 47.619 0.00 0.00 0.00 4.85
497 578 2.393768 CGCTGCAATGGAGCTTCGT 61.394 57.895 23.54 0.00 34.03 3.85
527 608 1.427020 GATGCTGCGTTGGAGCTTC 59.573 57.895 11.54 10.54 37.35 3.86
541 622 2.202492 CTTCGCCGGACTCTGTCG 60.202 66.667 5.05 0.00 32.65 4.35
547 628 2.126307 CGGACTCTGTCGGTGCTG 60.126 66.667 0.00 0.00 32.65 4.41
549 630 2.807045 GACTCTGTCGGTGCTGCG 60.807 66.667 0.00 0.00 0.00 5.18
560 641 2.669569 TGCTGCGTTGGAGCTTCC 60.670 61.111 11.54 0.00 37.35 3.46
582 663 0.899717 GGGGCTGCAATGGAACTTCA 60.900 55.000 0.50 0.00 0.00 3.02
602 683 3.681835 GGACTCCGTCGGTGCTGT 61.682 66.667 11.88 6.44 32.65 4.40
615 696 2.555199 GGTGCTGTGTTGGAGCTATAG 58.445 52.381 0.00 0.00 37.35 1.31
621 702 2.823747 TGTGTTGGAGCTATAGACACGT 59.176 45.455 3.21 0.00 42.53 4.49
628 709 3.066342 GGAGCTATAGACACGTTGCACTA 59.934 47.826 3.21 0.00 0.00 2.74
646 727 1.400846 CTATGCTGCAGTGGAGCTTTG 59.599 52.381 32.76 24.05 37.35 2.77
648 729 2.960170 CTGCAGTGGAGCTTTGCC 59.040 61.111 5.25 0.00 37.03 4.52
687 768 1.578423 GTTGAAGCTGGTCTGCTGC 59.422 57.895 3.20 2.27 43.24 5.25
693 774 4.007644 CTGGTCTGCTGCCGTGGA 62.008 66.667 0.00 0.00 0.00 4.02
736 817 0.885879 ACACGTTGATCTGACGGCTA 59.114 50.000 20.69 0.00 44.34 3.93
741 822 2.098607 CGTTGATCTGACGGCTAGGTAA 59.901 50.000 12.47 0.00 36.90 2.85
742 823 3.707793 GTTGATCTGACGGCTAGGTAAG 58.292 50.000 0.00 0.00 0.00 2.34
783 864 1.068541 TCATCCGGCTGATTCGTATCG 60.069 52.381 3.28 0.00 33.23 2.92
795 876 1.483316 TCGTATCGTGCGCCATAAAG 58.517 50.000 4.18 0.00 0.00 1.85
797 878 1.189446 CGTATCGTGCGCCATAAAGAC 59.811 52.381 4.18 0.00 0.00 3.01
814 895 8.540492 CCATAAAGACACACGATACACTATTTC 58.460 37.037 0.00 0.00 0.00 2.17
818 899 8.603242 AAGACACACGATACACTATTTCTTTT 57.397 30.769 0.00 0.00 0.00 2.27
819 900 8.018677 AGACACACGATACACTATTTCTTTTG 57.981 34.615 0.00 0.00 0.00 2.44
1016 1097 1.066002 ACACATGCGCAATAATCTGCC 59.934 47.619 17.11 0.00 39.26 4.85
1023 1104 0.308993 GCAATAATCTGCCGTCTGCC 59.691 55.000 0.00 0.00 40.16 4.85
1048 1129 1.006571 TTCGACCCACGCTTGTCTC 60.007 57.895 0.00 0.00 42.26 3.36
1049 1130 2.430382 TTCGACCCACGCTTGTCTCC 62.430 60.000 0.00 0.00 42.26 3.71
1051 1132 2.526873 ACCCACGCTTGTCTCCCT 60.527 61.111 0.00 0.00 0.00 4.20
1052 1133 2.266055 CCCACGCTTGTCTCCCTC 59.734 66.667 0.00 0.00 0.00 4.30
1056 1137 3.003173 CGCTTGTCTCCCTCCCCA 61.003 66.667 0.00 0.00 0.00 4.96
1089 1170 1.550976 CTCTCTAGTCCCCACCACAAC 59.449 57.143 0.00 0.00 0.00 3.32
1612 1700 2.093235 GTGGAGATTGTGGAGAAGGAGG 60.093 54.545 0.00 0.00 0.00 4.30
1701 1789 0.040942 CCCACCATCACCCCATTCAA 59.959 55.000 0.00 0.00 0.00 2.69
1742 1830 6.668323 TGCTGAACTCTGTTATTTACTTTGC 58.332 36.000 0.00 0.00 0.00 3.68
1743 1831 5.790495 GCTGAACTCTGTTATTTACTTTGCG 59.210 40.000 0.00 0.00 0.00 4.85
1746 1834 8.094798 TGAACTCTGTTATTTACTTTGCGAAT 57.905 30.769 0.00 0.00 0.00 3.34
1800 1888 1.093972 TATGCTGCCATTGGTTGACG 58.906 50.000 4.26 0.00 32.85 4.35
1809 1897 0.768622 ATTGGTTGACGGGAGGACAA 59.231 50.000 0.00 0.00 0.00 3.18
1814 1902 1.134491 GTTGACGGGAGGACAATAGGG 60.134 57.143 0.00 0.00 34.21 3.53
1841 1929 6.830324 TGTTGAGAATAGCTGAGGCATTTTAT 59.170 34.615 0.00 0.00 41.70 1.40
1850 1938 4.866486 GCTGAGGCATTTTATTGTCTTTGG 59.134 41.667 0.00 0.00 38.54 3.28
2091 2183 4.765339 GGGAGCTTGTTGGTTATTACAACT 59.235 41.667 9.36 0.00 46.28 3.16
2374 2476 4.471904 ACGTGAAAGGATGCTTATCTCA 57.528 40.909 0.00 0.00 0.00 3.27
2499 2601 3.073735 AGCTGAGCTGTCCGGGAG 61.074 66.667 5.97 0.00 37.57 4.30
2506 2608 0.896226 AGCTGTCCGGGAGTAAGAAC 59.104 55.000 0.00 0.00 0.00 3.01
2507 2609 0.108281 GCTGTCCGGGAGTAAGAACC 60.108 60.000 0.00 0.00 0.00 3.62
2510 2612 1.203087 TGTCCGGGAGTAAGAACCTGA 60.203 52.381 0.00 0.00 34.76 3.86
2529 2631 0.613012 AATTCTGGGGCTGCTGTTCC 60.613 55.000 0.00 0.00 0.00 3.62
2625 2730 3.900966 TGACATGGTCCTTCATGAGAG 57.099 47.619 11.20 0.00 45.30 3.20
2639 2744 3.250762 TCATGAGAGCACAAAAACGAAGG 59.749 43.478 0.00 0.00 0.00 3.46
2647 2752 5.474825 AGCACAAAAACGAAGGAAAAAGAA 58.525 33.333 0.00 0.00 0.00 2.52
2649 2754 5.347635 GCACAAAAACGAAGGAAAAAGAAGT 59.652 36.000 0.00 0.00 0.00 3.01
2798 2903 8.510505 AGAAAAAGAAATCAACTAGAGCATCAC 58.489 33.333 0.00 0.00 37.82 3.06
2808 2913 1.216064 AGAGCATCACCAAGGGCATA 58.784 50.000 0.00 0.00 37.82 3.14
2833 2938 2.229062 GAGTAAGCCTGCAAGAAAACCC 59.771 50.000 0.00 0.00 34.07 4.11
2846 2951 3.344515 AGAAAACCCGCTGGAAGTAATC 58.655 45.455 0.00 0.00 35.30 1.75
2898 3003 4.570874 GGGGGATCCTGCTTCGGC 62.571 72.222 12.58 0.00 42.19 5.54
2935 3040 3.381590 GGCCTTTGGGTCAATATGACTTC 59.618 47.826 10.06 4.49 46.19 3.01
2936 3041 4.273318 GCCTTTGGGTCAATATGACTTCT 58.727 43.478 10.06 0.00 46.19 2.85
2953 3058 5.096443 ACTTCTCAAGTTCCATCCTCATC 57.904 43.478 0.00 0.00 39.04 2.92
3032 3137 6.628856 CACTGAACAACTACACAAAGAATTCG 59.371 38.462 0.00 0.00 0.00 3.34
3265 3370 1.818642 GTGAATCTGCAGAGGCTTGT 58.181 50.000 22.96 0.23 41.91 3.16
3313 3418 3.201290 AGCTATTTCTTCAGGCACATCG 58.799 45.455 0.00 0.00 0.00 3.84
3356 3461 8.564574 GTGAACATATTTTCTGTAACCTTGTGA 58.435 33.333 3.41 0.00 0.00 3.58
3363 3468 6.633500 TTTCTGTAACCTTGTGATCCTTTG 57.367 37.500 0.00 0.00 0.00 2.77
3422 3531 5.620206 TGAAGCTTCCTGAATACAGTTTCA 58.380 37.500 23.42 0.00 42.05 2.69
3431 3540 4.469657 TGAATACAGTTTCAAAGGCAGGT 58.530 39.130 0.00 0.00 32.82 4.00
3451 3560 5.410746 CAGGTATCATCATATTGCCTGACAC 59.589 44.000 3.13 0.00 43.22 3.67
3495 3604 5.263599 AGAATGTCCATGGCAAAGATACAA 58.736 37.500 6.96 0.00 0.00 2.41
3605 3714 1.227999 ATTCTTGGCACGACACACCG 61.228 55.000 0.00 0.00 0.00 4.94
3643 3752 9.173939 CAGTTTAACAGTAAGCATTTTTGAGAG 57.826 33.333 0.00 0.00 0.00 3.20
3768 3878 4.469945 GGATGGATATCCCGGTCATCTTTA 59.530 45.833 19.34 0.00 46.03 1.85
3807 3917 4.263018 TGATGACAGTTCTGTGGAAGAG 57.737 45.455 10.29 0.00 35.91 2.85
4045 4155 7.936847 TGGTCCAAATATATACTTTGCTACCTG 59.063 37.037 21.54 9.49 38.10 4.00
4046 4156 7.390718 GGTCCAAATATATACTTTGCTACCTGG 59.609 40.741 18.41 0.00 36.35 4.45
4057 4167 3.185880 TGCTACCTGGAGTCCTAAACT 57.814 47.619 11.33 0.00 42.42 2.66
4086 4196 9.754382 CTTGCATATCAATGTTTTTAGGCTTAT 57.246 29.630 0.00 0.00 35.38 1.73
4121 4231 7.040617 GGAACAGAATACCGATCACTACTATCA 60.041 40.741 0.00 0.00 0.00 2.15
4133 4243 4.690748 TCACTACTATCAGCAAACAACAGC 59.309 41.667 0.00 0.00 0.00 4.40
4135 4245 1.806542 ACTATCAGCAAACAACAGCCG 59.193 47.619 0.00 0.00 0.00 5.52
4213 4323 9.146586 ACAATATAAAATGGGTAGAATGTGCAT 57.853 29.630 0.00 0.00 0.00 3.96
4301 4411 8.824756 TGTTTGTATCTGTCTTCTCCTATACT 57.175 34.615 0.00 0.00 0.00 2.12
4319 4429 1.202976 ACTTGGAACCTCTGCTGCATT 60.203 47.619 1.31 0.00 0.00 3.56
4346 4456 2.616256 CCTGGCTAACATCAACTCAGCA 60.616 50.000 0.00 0.00 33.86 4.41
4351 4461 5.355071 TGGCTAACATCAACTCAGCATAAAG 59.645 40.000 0.00 0.00 33.86 1.85
4390 4502 6.329496 GCTTGATGCTAGTATCTGATACTCC 58.671 44.000 28.44 21.29 44.55 3.85
4391 4503 6.627065 GCTTGATGCTAGTATCTGATACTCCC 60.627 46.154 28.44 21.01 44.55 4.30
4392 4504 6.146140 TGATGCTAGTATCTGATACTCCCT 57.854 41.667 28.44 16.05 44.55 4.20
4393 4505 6.184068 TGATGCTAGTATCTGATACTCCCTC 58.816 44.000 28.44 21.62 44.55 4.30
4394 4506 4.924625 TGCTAGTATCTGATACTCCCTCC 58.075 47.826 28.44 15.75 44.55 4.30
4395 4507 4.604050 TGCTAGTATCTGATACTCCCTCCT 59.396 45.833 28.44 10.30 44.55 3.69
4396 4508 5.791141 TGCTAGTATCTGATACTCCCTCCTA 59.209 44.000 28.44 12.31 44.55 2.94
4397 4509 6.448714 TGCTAGTATCTGATACTCCCTCCTAT 59.551 42.308 28.44 9.05 44.55 2.57
4398 4510 6.996282 GCTAGTATCTGATACTCCCTCCTATC 59.004 46.154 28.44 6.60 44.55 2.08
4399 4511 6.335781 AGTATCTGATACTCCCTCCTATCC 57.664 45.833 21.61 0.00 42.17 2.59
4400 4512 5.798518 AGTATCTGATACTCCCTCCTATCCA 59.201 44.000 21.61 0.00 42.17 3.41
4401 4513 5.829858 ATCTGATACTCCCTCCTATCCAT 57.170 43.478 0.00 0.00 0.00 3.41
4402 4514 4.940483 TCTGATACTCCCTCCTATCCATG 58.060 47.826 0.00 0.00 0.00 3.66
4403 4515 4.358310 TCTGATACTCCCTCCTATCCATGT 59.642 45.833 0.00 0.00 0.00 3.21
4404 4516 5.090139 CTGATACTCCCTCCTATCCATGTT 58.910 45.833 0.00 0.00 0.00 2.71
4405 4517 6.046762 TCTGATACTCCCTCCTATCCATGTTA 59.953 42.308 0.00 0.00 0.00 2.41
4406 4518 6.630131 TGATACTCCCTCCTATCCATGTTAA 58.370 40.000 0.00 0.00 0.00 2.01
4407 4519 7.256399 TGATACTCCCTCCTATCCATGTTAAT 58.744 38.462 0.00 0.00 0.00 1.40
4408 4520 7.739444 TGATACTCCCTCCTATCCATGTTAATT 59.261 37.037 0.00 0.00 0.00 1.40
4409 4521 6.192970 ACTCCCTCCTATCCATGTTAATTG 57.807 41.667 0.00 0.00 0.00 2.32
4410 4522 5.672194 ACTCCCTCCTATCCATGTTAATTGT 59.328 40.000 0.00 0.00 0.00 2.71
4411 4523 6.183361 ACTCCCTCCTATCCATGTTAATTGTC 60.183 42.308 0.00 0.00 0.00 3.18
4412 4524 5.669904 TCCCTCCTATCCATGTTAATTGTCA 59.330 40.000 0.00 0.00 0.00 3.58
4413 4525 5.765182 CCCTCCTATCCATGTTAATTGTCAC 59.235 44.000 0.00 0.00 0.00 3.67
4414 4526 6.409695 CCCTCCTATCCATGTTAATTGTCACT 60.410 42.308 0.00 0.00 0.00 3.41
4415 4527 6.484643 CCTCCTATCCATGTTAATTGTCACTG 59.515 42.308 0.00 0.00 0.00 3.66
4416 4528 7.194112 TCCTATCCATGTTAATTGTCACTGA 57.806 36.000 0.00 0.00 0.00 3.41
4417 4529 7.805163 TCCTATCCATGTTAATTGTCACTGAT 58.195 34.615 0.00 0.00 0.00 2.90
4418 4530 8.274322 TCCTATCCATGTTAATTGTCACTGATT 58.726 33.333 0.00 0.00 0.00 2.57
4419 4531 8.906867 CCTATCCATGTTAATTGTCACTGATTT 58.093 33.333 0.00 0.00 0.00 2.17
4422 4534 8.862325 TCCATGTTAATTGTCACTGATTTAGT 57.138 30.769 0.00 0.00 41.36 2.24
4423 4535 9.952030 TCCATGTTAATTGTCACTGATTTAGTA 57.048 29.630 0.00 0.00 37.60 1.82
4424 4536 9.988350 CCATGTTAATTGTCACTGATTTAGTAC 57.012 33.333 0.00 0.00 37.60 2.73
4431 4543 9.998106 AATTGTCACTGATTTAGTACAACTACT 57.002 29.630 0.00 0.00 37.60 2.57
4442 4554 8.679288 TTTAGTACAACTACTAAATCAGCGAC 57.321 34.615 8.39 0.00 44.93 5.19
4443 4555 6.263516 AGTACAACTACTAAATCAGCGACA 57.736 37.500 0.00 0.00 30.81 4.35
4444 4556 6.684686 AGTACAACTACTAAATCAGCGACAA 58.315 36.000 0.00 0.00 30.81 3.18
4445 4557 7.321153 AGTACAACTACTAAATCAGCGACAAT 58.679 34.615 0.00 0.00 30.81 2.71
4446 4558 7.817962 AGTACAACTACTAAATCAGCGACAATT 59.182 33.333 0.00 0.00 30.81 2.32
4447 4559 9.079833 GTACAACTACTAAATCAGCGACAATTA 57.920 33.333 0.00 0.00 0.00 1.40
4448 4560 8.542497 ACAACTACTAAATCAGCGACAATTAA 57.458 30.769 0.00 0.00 0.00 1.40
4449 4561 9.162764 ACAACTACTAAATCAGCGACAATTAAT 57.837 29.630 0.00 0.00 0.00 1.40
4454 4566 8.902540 ACTAAATCAGCGACAATTAATATGGA 57.097 30.769 0.00 0.00 0.00 3.41
4455 4567 9.507329 ACTAAATCAGCGACAATTAATATGGAT 57.493 29.630 0.00 0.00 0.00 3.41
4456 4568 9.979270 CTAAATCAGCGACAATTAATATGGATC 57.021 33.333 0.00 0.00 0.00 3.36
4457 4569 6.653273 ATCAGCGACAATTAATATGGATCG 57.347 37.500 0.00 0.00 0.00 3.69
4458 4570 4.929211 TCAGCGACAATTAATATGGATCGG 59.071 41.667 0.00 0.00 0.00 4.18
4459 4571 4.929211 CAGCGACAATTAATATGGATCGGA 59.071 41.667 0.00 0.00 0.00 4.55
4460 4572 5.062683 CAGCGACAATTAATATGGATCGGAG 59.937 44.000 0.00 0.00 0.00 4.63
4461 4573 4.330074 GCGACAATTAATATGGATCGGAGG 59.670 45.833 0.00 0.00 0.00 4.30
4462 4574 4.870426 CGACAATTAATATGGATCGGAGGG 59.130 45.833 0.00 0.00 0.00 4.30
4463 4575 5.337250 CGACAATTAATATGGATCGGAGGGA 60.337 44.000 0.00 0.00 0.00 4.20
4464 4576 6.054860 ACAATTAATATGGATCGGAGGGAG 57.945 41.667 0.00 0.00 0.00 4.30
4465 4577 4.762289 ATTAATATGGATCGGAGGGAGC 57.238 45.455 0.00 0.00 0.00 4.70
4466 4578 2.030027 AATATGGATCGGAGGGAGCA 57.970 50.000 0.00 0.00 30.89 4.26
4476 4588 1.401905 CGGAGGGAGCAACTATTTTGC 59.598 52.381 0.58 0.58 45.22 3.68
4529 4641 3.181488 TGCACCATGCTTTTGGATAATCG 60.181 43.478 7.74 0.00 45.31 3.34
4622 4734 2.097036 CTGAGATCAAGGCAATGGCAA 58.903 47.619 10.05 0.00 43.71 4.52
4626 4738 1.547372 GATCAAGGCAATGGCAACTGT 59.453 47.619 10.05 0.00 43.71 3.55
4646 4758 1.865865 TGGTTCTTGTTCTGCTCGAC 58.134 50.000 0.00 0.00 0.00 4.20
4703 4815 4.175516 CAGTGATCTCAGACTCAAAGCTC 58.824 47.826 0.00 0.00 0.00 4.09
4775 4896 4.265073 AGGATGCCTATGTGTTTCTTGAC 58.735 43.478 0.00 0.00 28.47 3.18
4865 4986 1.137282 GTCGACCTCATCCTCCCTTTC 59.863 57.143 3.51 0.00 0.00 2.62
4874 4995 1.497161 TCCTCCCTTTCGGAAGATCC 58.503 55.000 4.56 0.00 41.40 3.36
4904 5025 2.081462 CCCATGTCAAGTTAACCCGTC 58.919 52.381 0.88 0.00 0.00 4.79
4905 5026 2.081462 CCATGTCAAGTTAACCCGTCC 58.919 52.381 0.88 0.00 0.00 4.79
4913 5034 3.121738 AGTTAACCCGTCCAAGAAGTG 57.878 47.619 0.88 0.00 0.00 3.16
4916 5037 0.818040 AACCCGTCCAAGAAGTGCAC 60.818 55.000 9.40 9.40 0.00 4.57
4924 5048 2.086869 CCAAGAAGTGCACCATAGTGG 58.913 52.381 14.63 11.25 44.69 4.00
4936 5068 4.700213 GCACCATAGTGGACAGTAACAATT 59.300 41.667 2.45 0.00 44.69 2.32
4939 5071 7.327975 CACCATAGTGGACAGTAACAATTCTA 58.672 38.462 2.45 0.00 40.96 2.10
4940 5072 7.277981 CACCATAGTGGACAGTAACAATTCTAC 59.722 40.741 2.45 0.00 40.96 2.59
4943 5075 5.548406 AGTGGACAGTAACAATTCTACACC 58.452 41.667 0.00 0.00 0.00 4.16
4944 5076 5.071250 AGTGGACAGTAACAATTCTACACCA 59.929 40.000 0.00 0.00 0.00 4.17
4945 5077 5.178809 GTGGACAGTAACAATTCTACACCAC 59.821 44.000 0.00 0.00 35.41 4.16
4946 5078 4.387862 GGACAGTAACAATTCTACACCACG 59.612 45.833 0.00 0.00 0.00 4.94
4947 5079 3.744426 ACAGTAACAATTCTACACCACGC 59.256 43.478 0.00 0.00 0.00 5.34
4948 5080 2.991190 AGTAACAATTCTACACCACGCG 59.009 45.455 3.53 3.53 0.00 6.01
4963 5095 0.667487 ACGCGCAGGATTCGGATATG 60.667 55.000 5.73 0.00 0.00 1.78
4968 5100 3.849911 CGCAGGATTCGGATATGTATGT 58.150 45.455 0.00 0.00 0.00 2.29
4978 5110 3.005791 CGGATATGTATGTCCACTCAGCA 59.994 47.826 8.16 0.00 37.89 4.41
4999 5131 3.495377 CAGAGTAGATAGAAGTCGTCCCG 59.505 52.174 0.00 0.00 0.00 5.14
5023 5155 1.008881 GCATCAGCGGCATGACATG 60.009 57.895 11.27 11.27 30.46 3.21
5057 5189 1.377725 CACAGTGACAGCCCCCATC 60.378 63.158 0.00 0.00 0.00 3.51
5068 5201 1.302832 CCCCCATCGGCTTGCTATC 60.303 63.158 0.00 0.00 0.00 2.08
5069 5202 1.757306 CCCCATCGGCTTGCTATCT 59.243 57.895 0.00 0.00 0.00 1.98
5070 5203 0.976641 CCCCATCGGCTTGCTATCTA 59.023 55.000 0.00 0.00 0.00 1.98
5113 5246 3.715495 TGCTTTACCATTGCTTGTTGTG 58.285 40.909 0.00 0.00 0.00 3.33
5118 5251 3.163630 ACCATTGCTTGTTGTGTGTTC 57.836 42.857 0.00 0.00 0.00 3.18
5241 5411 4.615223 CGTAGTGTATCATATCACCACGGG 60.615 50.000 7.97 0.00 42.44 5.28
5244 5414 2.703536 TGTATCATATCACCACGGGCTT 59.296 45.455 0.00 0.00 0.00 4.35
5253 5423 3.777925 CACGGGCTTGCGTTCTCG 61.778 66.667 0.00 0.00 40.37 4.04
5275 5447 0.856490 CGTCGTAGTGCGTCTGTAGC 60.856 60.000 0.00 0.00 42.13 3.58
5276 5448 0.447011 GTCGTAGTGCGTCTGTAGCT 59.553 55.000 0.00 0.00 42.13 3.32
5277 5449 0.446616 TCGTAGTGCGTCTGTAGCTG 59.553 55.000 0.00 0.00 42.13 4.24
5278 5450 0.168348 CGTAGTGCGTCTGTAGCTGT 59.832 55.000 0.00 0.00 35.54 4.40
5279 5451 1.395954 CGTAGTGCGTCTGTAGCTGTA 59.604 52.381 0.00 0.00 35.54 2.74
5280 5452 2.537128 CGTAGTGCGTCTGTAGCTGTAG 60.537 54.545 0.00 0.00 35.54 2.74
5316 5488 4.447138 AACCATTTGACTCTTGTGGGTA 57.553 40.909 0.00 0.00 34.27 3.69
5356 5535 3.695606 TCACCTGACTGGCCGAGC 61.696 66.667 0.00 0.00 40.22 5.03
5420 5611 1.787155 CGTCGCTGTATGGCTCAATAC 59.213 52.381 0.00 0.00 34.24 1.89
5421 5612 2.798145 CGTCGCTGTATGGCTCAATACA 60.798 50.000 7.07 7.07 40.01 2.29
5422 5613 3.194861 GTCGCTGTATGGCTCAATACAA 58.805 45.455 8.20 0.00 41.33 2.41
5512 5706 0.181114 TCTGGACTTTGCAGCTGTGT 59.819 50.000 16.64 9.37 35.65 3.72
5513 5707 1.416030 TCTGGACTTTGCAGCTGTGTA 59.584 47.619 16.64 0.00 35.65 2.90
5572 5770 1.470098 CGCTGCAGCTGATTTTTAGGT 59.530 47.619 34.22 0.00 39.32 3.08
5613 5813 1.275573 GACAGGCTTCGGAAAGGTAGT 59.724 52.381 0.00 0.00 32.79 2.73
5620 5820 5.659971 AGGCTTCGGAAAGGTAGTAGAATTA 59.340 40.000 0.00 0.00 32.79 1.40
5637 5837 6.163135 AGAATTATTCTTGACGACTAGGGG 57.837 41.667 0.99 0.00 36.36 4.79
5641 5841 2.005370 TCTTGACGACTAGGGGTTGT 57.995 50.000 0.00 0.00 44.62 3.32
5645 5845 2.596346 TGACGACTAGGGGTTGTGTTA 58.404 47.619 0.00 0.00 42.21 2.41
5646 5846 2.559668 TGACGACTAGGGGTTGTGTTAG 59.440 50.000 0.00 0.00 42.21 2.34
5678 5878 0.977395 GAGCTGTGGGTTAGGTGAGT 59.023 55.000 0.00 0.00 0.00 3.41
5679 5879 0.687354 AGCTGTGGGTTAGGTGAGTG 59.313 55.000 0.00 0.00 0.00 3.51
5680 5880 0.685097 GCTGTGGGTTAGGTGAGTGA 59.315 55.000 0.00 0.00 0.00 3.41
5764 5964 4.456222 CGGATCGAGATAGTGGTATGTTCT 59.544 45.833 0.00 0.00 0.00 3.01
5777 5977 7.402862 AGTGGTATGTTCTGCTAAATTTACCT 58.597 34.615 0.00 0.00 31.30 3.08
5793 5993 4.978083 TTACCTCTACCGCTAAGTCTTG 57.022 45.455 0.00 0.00 0.00 3.02
5805 6005 4.006319 GCTAAGTCTTGTCTGGCTTCATT 58.994 43.478 0.00 0.00 0.00 2.57
5806 6006 4.094146 GCTAAGTCTTGTCTGGCTTCATTC 59.906 45.833 0.00 0.00 0.00 2.67
5807 6007 3.777106 AGTCTTGTCTGGCTTCATTCA 57.223 42.857 0.00 0.00 0.00 2.57
5808 6008 3.406764 AGTCTTGTCTGGCTTCATTCAC 58.593 45.455 0.00 0.00 0.00 3.18
5842 6042 6.237901 CACCTGCTACTCTATGATCTCTAGT 58.762 44.000 0.00 0.00 0.00 2.57
5859 6059 5.300286 TCTCTAGTTGATGATGAAGCATCGA 59.700 40.000 4.27 0.00 45.93 3.59
5865 6065 5.473066 TGATGATGAAGCATCGATCCTAA 57.527 39.130 0.00 0.00 45.93 2.69
5873 6073 6.785191 TGAAGCATCGATCCTAATTTTTCAC 58.215 36.000 0.00 0.00 0.00 3.18
5883 6083 8.818057 CGATCCTAATTTTTCACGAAGAGTTAT 58.182 33.333 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.772624 AGAGTAGCATTATAAGGCCATCGA 59.227 41.667 17.92 0.00 36.12 3.59
14 15 5.630415 AACAGAGTAGCATTATAAGGCCA 57.370 39.130 17.92 1.94 36.12 5.36
19 20 7.064134 CGGTGTTGAAACAGAGTAGCATTATAA 59.936 37.037 0.00 0.00 40.05 0.98
20 21 6.533723 CGGTGTTGAAACAGAGTAGCATTATA 59.466 38.462 0.00 0.00 40.05 0.98
23 24 3.498397 CGGTGTTGAAACAGAGTAGCATT 59.502 43.478 0.00 0.00 40.05 3.56
26 27 1.194772 GCGGTGTTGAAACAGAGTAGC 59.805 52.381 0.00 0.00 40.05 3.58
35 36 1.076632 AACAGGGGCGGTGTTGAAA 60.077 52.632 2.60 0.00 36.76 2.69
36 37 2.598467 AACAGGGGCGGTGTTGAA 59.402 55.556 2.60 0.00 36.76 2.69
45 46 0.532115 CCTATGTTTGCAACAGGGGC 59.468 55.000 0.00 0.00 45.95 5.80
46 47 1.185315 CCCTATGTTTGCAACAGGGG 58.815 55.000 19.96 19.16 45.95 4.79
66 67 1.679032 GGTAGTAGGGTGGCTGCTTTG 60.679 57.143 0.00 0.00 0.00 2.77
67 68 0.618981 GGTAGTAGGGTGGCTGCTTT 59.381 55.000 0.00 0.00 0.00 3.51
68 69 0.546747 TGGTAGTAGGGTGGCTGCTT 60.547 55.000 0.00 0.00 0.00 3.91
78 79 0.032678 CTGCGAGCCATGGTAGTAGG 59.967 60.000 14.67 0.00 0.00 3.18
81 82 1.680522 CTCCTGCGAGCCATGGTAGT 61.681 60.000 14.67 0.00 0.00 2.73
84 85 3.005539 ACTCCTGCGAGCCATGGT 61.006 61.111 14.67 0.00 40.03 3.55
86 87 2.584418 CGACTCCTGCGAGCCATG 60.584 66.667 0.00 0.00 40.03 3.66
87 88 4.521062 GCGACTCCTGCGAGCCAT 62.521 66.667 0.00 0.00 40.03 4.40
89 90 4.742201 TTGCGACTCCTGCGAGCC 62.742 66.667 0.00 0.00 40.03 4.70
90 91 3.482783 GTTGCGACTCCTGCGAGC 61.483 66.667 0.00 0.00 40.03 5.03
91 92 2.811317 GGTTGCGACTCCTGCGAG 60.811 66.667 3.59 0.00 42.32 5.03
92 93 4.717629 CGGTTGCGACTCCTGCGA 62.718 66.667 3.59 0.00 34.24 5.10
103 104 1.831343 CTTGCATCAATAGCGGTTGC 58.169 50.000 0.00 0.00 43.24 4.17
104 105 1.132834 TGCTTGCATCAATAGCGGTTG 59.867 47.619 0.00 0.00 37.73 3.77
105 106 1.462616 TGCTTGCATCAATAGCGGTT 58.537 45.000 0.00 0.00 37.73 4.44
106 107 1.133025 GTTGCTTGCATCAATAGCGGT 59.867 47.619 3.06 0.00 37.73 5.68
111 114 3.081061 ACCTTCGTTGCTTGCATCAATA 58.919 40.909 5.39 0.00 0.00 1.90
117 120 1.227409 TCGACCTTCGTTGCTTGCA 60.227 52.632 0.00 0.00 41.35 4.08
125 128 2.023414 TTGCCAGTGTCGACCTTCGT 62.023 55.000 14.12 0.00 41.35 3.85
126 129 1.300620 TTGCCAGTGTCGACCTTCG 60.301 57.895 14.12 3.73 42.10 3.79
139 143 2.731721 CGTGTCGTAGCGTTGCCA 60.732 61.111 0.00 0.00 0.00 4.92
146 150 3.011760 GCTGCAACCGTGTCGTAGC 62.012 63.158 0.00 0.00 0.00 3.58
152 157 2.124320 ACCTTGCTGCAACCGTGT 60.124 55.556 11.69 3.80 0.00 4.49
154 159 2.972505 CGACCTTGCTGCAACCGT 60.973 61.111 11.69 10.37 0.00 4.83
231 236 1.722464 CAAAACACATGGATTGCAGCG 59.278 47.619 0.00 0.00 0.00 5.18
385 392 1.264288 GAGTAGCAGTGGTGTTGTTGC 59.736 52.381 4.76 0.00 36.83 4.17
541 622 2.970974 GAAGCTCCAACGCAGCACC 61.971 63.158 0.00 0.00 39.56 5.01
547 628 2.747855 CCAGGGAAGCTCCAACGC 60.748 66.667 0.00 0.00 38.64 4.84
549 630 2.356667 CCCCAGGGAAGCTCCAAC 59.643 66.667 7.25 0.00 38.64 3.77
560 641 2.037687 TTCCATTGCAGCCCCAGG 59.962 61.111 0.00 0.00 0.00 4.45
602 683 3.845178 CAACGTGTCTATAGCTCCAACA 58.155 45.455 0.00 0.00 0.00 3.33
628 709 1.874345 GCAAAGCTCCACTGCAGCAT 61.874 55.000 15.27 0.00 39.56 3.79
687 768 2.390599 CGATGCACCAACTCCACGG 61.391 63.158 0.00 0.00 0.00 4.94
693 774 1.315257 GGCCATTCGATGCACCAACT 61.315 55.000 0.00 0.00 0.00 3.16
732 813 4.804261 ATGAAATCATCCGCTTACCTAGCC 60.804 45.833 0.00 0.00 38.20 3.93
736 817 5.070446 TGTCTATGAAATCATCCGCTTACCT 59.930 40.000 0.00 0.00 37.76 3.08
741 822 6.057533 TGATTTGTCTATGAAATCATCCGCT 58.942 36.000 0.00 0.00 42.29 5.52
742 823 6.304356 TGATTTGTCTATGAAATCATCCGC 57.696 37.500 0.00 0.00 42.29 5.54
795 876 8.014322 TCAAAAGAAATAGTGTATCGTGTGTC 57.986 34.615 0.00 0.00 0.00 3.67
797 878 8.162880 GTCTCAAAAGAAATAGTGTATCGTGTG 58.837 37.037 0.00 0.00 31.93 3.82
814 895 9.103048 GTGTATCGTGTTATTTTGTCTCAAAAG 57.897 33.333 12.07 0.53 0.00 2.27
818 899 8.918658 GTTAGTGTATCGTGTTATTTTGTCTCA 58.081 33.333 0.00 0.00 0.00 3.27
819 900 8.918658 TGTTAGTGTATCGTGTTATTTTGTCTC 58.081 33.333 0.00 0.00 0.00 3.36
969 1050 1.152546 GGGCTATTTTGGGGGCGAT 60.153 57.895 0.00 0.00 0.00 4.58
1023 1104 2.805353 CGTGGGTCGAAGCAGACG 60.805 66.667 0.00 0.00 41.81 4.18
1030 1111 1.006571 GAGACAAGCGTGGGTCGAA 60.007 57.895 4.26 0.00 42.86 3.71
1031 1112 2.649034 GAGACAAGCGTGGGTCGA 59.351 61.111 4.26 0.00 42.86 4.20
1048 1129 1.359130 AGTTTGGAGATTTGGGGAGGG 59.641 52.381 0.00 0.00 0.00 4.30
1049 1130 2.310052 AGAGTTTGGAGATTTGGGGAGG 59.690 50.000 0.00 0.00 0.00 4.30
1051 1132 3.260205 AGAGAGTTTGGAGATTTGGGGA 58.740 45.455 0.00 0.00 0.00 4.81
1052 1133 3.265479 AGAGAGAGTTTGGAGATTTGGGG 59.735 47.826 0.00 0.00 0.00 4.96
1056 1137 5.423931 GGGACTAGAGAGAGTTTGGAGATTT 59.576 44.000 0.00 0.00 0.00 2.17
1626 1714 3.978723 CTCCTGCAGCGTCACCTCG 62.979 68.421 8.66 0.00 0.00 4.63
1685 1773 2.291800 CCTTCTTGAATGGGGTGATGGT 60.292 50.000 0.00 0.00 0.00 3.55
1701 1789 4.401022 TCAGCATGAAACAATCACCTTCT 58.599 39.130 0.00 0.00 45.97 2.85
1785 1873 1.303236 TCCCGTCAACCAATGGCAG 60.303 57.895 0.00 0.00 31.20 4.85
1800 1888 2.307686 TCAACAACCCTATTGTCCTCCC 59.692 50.000 0.00 0.00 0.00 4.30
1809 1897 5.163258 CCTCAGCTATTCTCAACAACCCTAT 60.163 44.000 0.00 0.00 0.00 2.57
1814 1902 3.338249 TGCCTCAGCTATTCTCAACAAC 58.662 45.455 0.00 0.00 40.80 3.32
1841 1929 0.178992 CTCCCAGCACCCAAAGACAA 60.179 55.000 0.00 0.00 0.00 3.18
1850 1938 1.818674 CCACATAAAACTCCCAGCACC 59.181 52.381 0.00 0.00 0.00 5.01
2144 2238 2.871096 AATTCCTAAAGGTGGTCGCA 57.129 45.000 0.00 0.00 36.34 5.10
2186 2284 7.931948 AGAACCTGAAATTTCTAAAGAAGACGA 59.068 33.333 18.64 0.00 35.21 4.20
2374 2476 1.886542 GACAAGCCGAACAAAGGGAAT 59.113 47.619 0.00 0.00 0.00 3.01
2420 2522 5.368145 TGAAATACAGAACACAAGCTCACT 58.632 37.500 0.00 0.00 0.00 3.41
2499 2601 3.017442 GCCCCAGAATTCAGGTTCTTAC 58.983 50.000 15.09 0.00 36.33 2.34
2506 2608 1.035932 CAGCAGCCCCAGAATTCAGG 61.036 60.000 9.87 9.87 0.00 3.86
2507 2609 0.323178 ACAGCAGCCCCAGAATTCAG 60.323 55.000 8.44 0.00 0.00 3.02
2510 2612 0.613012 GGAACAGCAGCCCCAGAATT 60.613 55.000 0.00 0.00 0.00 2.17
2529 2631 1.096967 TGCCATGCTATGTTCGCCAG 61.097 55.000 0.00 0.00 0.00 4.85
2607 2712 1.911357 TGCTCTCATGAAGGACCATGT 59.089 47.619 0.00 0.00 43.22 3.21
2625 2730 5.347635 ACTTCTTTTTCCTTCGTTTTTGTGC 59.652 36.000 0.00 0.00 0.00 4.57
2639 2744 9.614792 TGATAGGGCTTTATCTACTTCTTTTTC 57.385 33.333 9.72 0.00 32.44 2.29
2649 2754 9.574516 GGAAAATCTTTGATAGGGCTTTATCTA 57.425 33.333 9.72 2.07 32.44 1.98
2657 2762 5.394553 CCTGTTGGAAAATCTTTGATAGGGC 60.395 44.000 0.00 0.00 34.57 5.19
2798 2903 2.945668 GCTTACTCTTGTATGCCCTTGG 59.054 50.000 0.00 0.00 41.27 3.61
2808 2913 3.492102 TTCTTGCAGGCTTACTCTTGT 57.508 42.857 0.00 0.00 0.00 3.16
2833 2938 0.583438 CATGGCGATTACTTCCAGCG 59.417 55.000 0.00 0.00 32.78 5.18
2869 2974 4.084287 CAGGATCCCCCATAATGATTGTG 58.916 47.826 8.55 0.00 37.41 3.33
2898 3003 2.449137 AGGCCCTTGATCCATCTTTG 57.551 50.000 0.00 0.00 0.00 2.77
2935 3040 3.808466 TCGATGAGGATGGAACTTGAG 57.192 47.619 0.00 0.00 0.00 3.02
2936 3041 5.869649 TTATCGATGAGGATGGAACTTGA 57.130 39.130 8.54 0.00 0.00 3.02
2953 3058 4.081807 TGAGATGATGAGGGCTGATTATCG 60.082 45.833 0.00 0.00 27.74 2.92
3032 3137 2.561478 TCAAGGTCCACTGCTTTACC 57.439 50.000 0.00 0.00 0.00 2.85
3060 3165 2.528041 AACCTTCTCGTCACTTGTCC 57.472 50.000 0.00 0.00 0.00 4.02
3139 3244 3.140707 TCCCATTATCATCTGCCCATGTT 59.859 43.478 0.00 0.00 0.00 2.71
3265 3370 2.026641 GCTTCAATAAGGGCTGATGCA 58.973 47.619 0.00 0.00 40.57 3.96
3271 3376 1.684248 CCTGCAGCTTCAATAAGGGCT 60.684 52.381 8.66 0.00 32.98 5.19
3313 3418 1.003580 TCACCTGCATCTTCCACTTCC 59.996 52.381 0.00 0.00 0.00 3.46
3391 3500 3.795688 TCAGGAAGCTTCAGGTCATTT 57.204 42.857 27.02 0.22 0.00 2.32
3393 3502 4.225942 TGTATTCAGGAAGCTTCAGGTCAT 59.774 41.667 27.02 13.98 0.00 3.06
3422 3531 4.768968 GGCAATATGATGATACCTGCCTTT 59.231 41.667 15.72 0.00 40.38 3.11
3431 3540 3.996363 GCGTGTCAGGCAATATGATGATA 59.004 43.478 12.54 0.00 0.00 2.15
3451 3560 1.070577 CGAACTGTTTCTGGTGAAGCG 60.071 52.381 0.00 0.00 36.40 4.68
3495 3604 7.918076 TCTGTTTCAGATACTACCTTTTCCAT 58.082 34.615 0.00 0.00 35.39 3.41
3605 3714 4.338400 ACTGTTAAACTGAAACCTTCTGGC 59.662 41.667 0.00 0.00 36.63 4.85
3684 3794 6.459670 TGAAAAGATATGCATGTCATTGCT 57.540 33.333 23.38 5.86 43.18 3.91
3768 3878 6.169094 GTCATCAAGCATGTATACATAGGCT 58.831 40.000 19.76 19.76 37.25 4.58
3807 3917 7.278875 ACTCTCTCCCATTAGAAATCAACATC 58.721 38.462 0.00 0.00 0.00 3.06
4045 4155 7.272978 TGATATGCAAGTAAGTTTAGGACTCC 58.727 38.462 0.00 0.00 37.72 3.85
4046 4156 8.718102 TTGATATGCAAGTAAGTTTAGGACTC 57.282 34.615 0.00 0.00 32.64 3.36
4057 4167 8.748412 AGCCTAAAAACATTGATATGCAAGTAA 58.252 29.630 0.00 0.00 40.42 2.24
4086 4196 4.951715 TCGGTATTCTGTTCCAGCTAGTAA 59.048 41.667 0.00 0.00 0.00 2.24
4087 4197 4.529897 TCGGTATTCTGTTCCAGCTAGTA 58.470 43.478 0.00 0.00 0.00 1.82
4088 4198 3.362706 TCGGTATTCTGTTCCAGCTAGT 58.637 45.455 0.00 0.00 0.00 2.57
4121 4231 1.226746 GTACTCGGCTGTTGTTTGCT 58.773 50.000 0.00 0.00 0.00 3.91
4133 4243 7.010552 CCAGAGTAATTTCTCAAATGTACTCGG 59.989 40.741 13.77 15.46 40.89 4.63
4135 4245 8.779354 ACCAGAGTAATTTCTCAAATGTACTC 57.221 34.615 13.77 15.07 39.10 2.59
4301 4411 1.074405 AGAATGCAGCAGAGGTTCCAA 59.926 47.619 0.00 0.00 0.00 3.53
4319 4429 4.985538 AGTTGATGTTAGCCAGGAAAAGA 58.014 39.130 0.00 0.00 0.00 2.52
4351 4461 6.066054 GCATCAAGCTAACCTATCTTTTCC 57.934 41.667 0.00 0.00 41.15 3.13
4378 4490 6.220609 ACATGGATAGGAGGGAGTATCAGATA 59.779 42.308 0.00 0.00 36.25 1.98
4387 4499 6.183361 TGACAATTAACATGGATAGGAGGGAG 60.183 42.308 0.00 0.00 0.00 4.30
4388 4500 5.669904 TGACAATTAACATGGATAGGAGGGA 59.330 40.000 0.00 0.00 0.00 4.20
4389 4501 5.765182 GTGACAATTAACATGGATAGGAGGG 59.235 44.000 0.00 0.00 0.00 4.30
4390 4502 6.484643 CAGTGACAATTAACATGGATAGGAGG 59.515 42.308 0.00 0.00 0.00 4.30
4391 4503 7.275183 TCAGTGACAATTAACATGGATAGGAG 58.725 38.462 0.00 0.00 0.00 3.69
4392 4504 7.194112 TCAGTGACAATTAACATGGATAGGA 57.806 36.000 0.00 0.00 0.00 2.94
4393 4505 8.455903 AATCAGTGACAATTAACATGGATAGG 57.544 34.615 0.00 0.00 0.00 2.57
4396 4508 9.466497 ACTAAATCAGTGACAATTAACATGGAT 57.534 29.630 0.00 0.00 35.62 3.41
4397 4509 8.862325 ACTAAATCAGTGACAATTAACATGGA 57.138 30.769 0.00 0.00 35.62 3.41
4398 4510 9.988350 GTACTAAATCAGTGACAATTAACATGG 57.012 33.333 0.00 0.00 38.24 3.66
4405 4517 9.998106 AGTAGTTGTACTAAATCAGTGACAATT 57.002 29.630 0.00 0.00 37.76 2.32
4418 4530 7.819644 TGTCGCTGATTTAGTAGTTGTACTAA 58.180 34.615 1.67 1.67 45.92 2.24
4419 4531 7.381766 TGTCGCTGATTTAGTAGTTGTACTA 57.618 36.000 0.00 0.00 40.23 1.82
4420 4532 6.263516 TGTCGCTGATTTAGTAGTTGTACT 57.736 37.500 0.00 0.00 42.49 2.73
4421 4533 6.939551 TTGTCGCTGATTTAGTAGTTGTAC 57.060 37.500 0.00 0.00 0.00 2.90
4422 4534 9.642327 TTAATTGTCGCTGATTTAGTAGTTGTA 57.358 29.630 0.00 0.00 0.00 2.41
4423 4535 8.542497 TTAATTGTCGCTGATTTAGTAGTTGT 57.458 30.769 0.00 0.00 0.00 3.32
4428 4540 9.990360 TCCATATTAATTGTCGCTGATTTAGTA 57.010 29.630 0.00 0.00 0.00 1.82
4429 4541 8.902540 TCCATATTAATTGTCGCTGATTTAGT 57.097 30.769 0.00 0.00 0.00 2.24
4430 4542 9.979270 GATCCATATTAATTGTCGCTGATTTAG 57.021 33.333 0.00 0.00 0.00 1.85
4431 4543 8.655970 CGATCCATATTAATTGTCGCTGATTTA 58.344 33.333 0.00 0.00 0.00 1.40
4432 4544 7.361201 CCGATCCATATTAATTGTCGCTGATTT 60.361 37.037 0.00 0.00 0.00 2.17
4433 4545 6.092670 CCGATCCATATTAATTGTCGCTGATT 59.907 38.462 0.00 0.00 0.00 2.57
4434 4546 5.582269 CCGATCCATATTAATTGTCGCTGAT 59.418 40.000 0.00 0.00 0.00 2.90
4435 4547 4.929211 CCGATCCATATTAATTGTCGCTGA 59.071 41.667 0.00 0.00 0.00 4.26
4436 4548 4.929211 TCCGATCCATATTAATTGTCGCTG 59.071 41.667 0.00 0.00 0.00 5.18
4437 4549 5.147330 TCCGATCCATATTAATTGTCGCT 57.853 39.130 0.00 0.00 0.00 4.93
4438 4550 4.330074 CCTCCGATCCATATTAATTGTCGC 59.670 45.833 0.00 0.00 0.00 5.19
4439 4551 4.870426 CCCTCCGATCCATATTAATTGTCG 59.130 45.833 0.00 0.00 0.00 4.35
4440 4552 6.049955 TCCCTCCGATCCATATTAATTGTC 57.950 41.667 0.00 0.00 0.00 3.18
4441 4553 5.571658 GCTCCCTCCGATCCATATTAATTGT 60.572 44.000 0.00 0.00 0.00 2.71
4442 4554 4.878397 GCTCCCTCCGATCCATATTAATTG 59.122 45.833 0.00 0.00 0.00 2.32
4443 4555 4.536090 TGCTCCCTCCGATCCATATTAATT 59.464 41.667 0.00 0.00 0.00 1.40
4444 4556 4.104086 TGCTCCCTCCGATCCATATTAAT 58.896 43.478 0.00 0.00 0.00 1.40
4445 4557 3.516586 TGCTCCCTCCGATCCATATTAA 58.483 45.455 0.00 0.00 0.00 1.40
4446 4558 3.184382 TGCTCCCTCCGATCCATATTA 57.816 47.619 0.00 0.00 0.00 0.98
4447 4559 2.030027 TGCTCCCTCCGATCCATATT 57.970 50.000 0.00 0.00 0.00 1.28
4448 4560 1.625818 GTTGCTCCCTCCGATCCATAT 59.374 52.381 0.00 0.00 0.00 1.78
4449 4561 1.048601 GTTGCTCCCTCCGATCCATA 58.951 55.000 0.00 0.00 0.00 2.74
4450 4562 0.692419 AGTTGCTCCCTCCGATCCAT 60.692 55.000 0.00 0.00 0.00 3.41
4451 4563 0.032515 TAGTTGCTCCCTCCGATCCA 60.033 55.000 0.00 0.00 0.00 3.41
4452 4564 1.343069 ATAGTTGCTCCCTCCGATCC 58.657 55.000 0.00 0.00 0.00 3.36
4453 4565 3.477210 AAATAGTTGCTCCCTCCGATC 57.523 47.619 0.00 0.00 0.00 3.69
4454 4566 3.545703 CAAAATAGTTGCTCCCTCCGAT 58.454 45.455 0.00 0.00 0.00 4.18
4455 4567 2.939640 GCAAAATAGTTGCTCCCTCCGA 60.940 50.000 3.85 0.00 41.87 4.55
4456 4568 1.401905 GCAAAATAGTTGCTCCCTCCG 59.598 52.381 3.85 0.00 41.87 4.63
4464 4576 4.479619 CAAGTGAGGAGCAAAATAGTTGC 58.520 43.478 2.85 2.85 45.22 4.17
4465 4577 4.022935 TGCAAGTGAGGAGCAAAATAGTTG 60.023 41.667 0.00 0.00 34.97 3.16
4466 4578 4.144297 TGCAAGTGAGGAGCAAAATAGTT 58.856 39.130 0.00 0.00 34.97 2.24
4476 4588 0.252479 ATGGCTCTGCAAGTGAGGAG 59.748 55.000 3.87 0.00 33.76 3.69
4477 4589 0.694771 AATGGCTCTGCAAGTGAGGA 59.305 50.000 3.87 0.00 33.76 3.71
4484 4596 3.374220 CAGAAACAAATGGCTCTGCAA 57.626 42.857 0.00 0.00 0.00 4.08
4529 4641 3.873952 GTGGCAACCAGATACTCTCATTC 59.126 47.826 0.00 0.00 32.34 2.67
4622 4734 2.945668 GAGCAGAACAAGAACCAACAGT 59.054 45.455 0.00 0.00 0.00 3.55
4626 4738 2.210116 GTCGAGCAGAACAAGAACCAA 58.790 47.619 0.00 0.00 0.00 3.67
4703 4815 2.443957 GAAACGCCACCTTCTGCACG 62.444 60.000 0.00 0.00 0.00 5.34
4876 4997 2.358125 TTGACATGGGCGTCACGG 60.358 61.111 0.00 0.00 45.36 4.94
4879 5000 2.147958 GTTAACTTGACATGGGCGTCA 58.852 47.619 0.00 0.00 44.05 4.35
4904 5025 2.086869 CCACTATGGTGCACTTCTTGG 58.913 52.381 17.98 12.89 41.75 3.61
4905 5026 2.744202 GTCCACTATGGTGCACTTCTTG 59.256 50.000 17.98 7.80 41.75 3.02
4913 5034 3.328382 TGTTACTGTCCACTATGGTGC 57.672 47.619 3.19 0.00 41.75 5.01
4916 5037 7.277981 GTGTAGAATTGTTACTGTCCACTATGG 59.722 40.741 0.00 0.00 39.43 2.74
4923 5047 4.387862 CGTGGTGTAGAATTGTTACTGTCC 59.612 45.833 0.00 0.00 0.00 4.02
4924 5048 4.143179 GCGTGGTGTAGAATTGTTACTGTC 60.143 45.833 0.00 0.00 0.00 3.51
4936 5068 1.884075 AATCCTGCGCGTGGTGTAGA 61.884 55.000 17.00 0.38 0.00 2.59
4939 5071 2.742372 GAATCCTGCGCGTGGTGT 60.742 61.111 17.00 7.85 0.00 4.16
4940 5072 3.853330 CGAATCCTGCGCGTGGTG 61.853 66.667 17.00 0.00 0.00 4.17
4943 5075 0.667487 ATATCCGAATCCTGCGCGTG 60.667 55.000 8.43 0.36 0.00 5.34
4944 5076 0.667487 CATATCCGAATCCTGCGCGT 60.667 55.000 8.43 0.00 0.00 6.01
4945 5077 0.667487 ACATATCCGAATCCTGCGCG 60.667 55.000 0.00 0.00 0.00 6.86
4946 5078 2.363788 TACATATCCGAATCCTGCGC 57.636 50.000 0.00 0.00 0.00 6.09
4947 5079 3.849911 ACATACATATCCGAATCCTGCG 58.150 45.455 0.00 0.00 0.00 5.18
4948 5080 4.184629 GGACATACATATCCGAATCCTGC 58.815 47.826 0.00 0.00 0.00 4.85
4999 5131 0.516001 CATGCCGCTGATGCTGATAC 59.484 55.000 0.00 0.00 36.97 2.24
5023 5155 1.017177 TGTGGCGGTATTTGAGTCGC 61.017 55.000 0.00 0.00 46.35 5.19
5057 5189 4.569761 TGTTCTAGTAGATAGCAAGCCG 57.430 45.455 0.00 0.00 0.00 5.52
5068 5201 7.675870 GCAGCAAGATTTGTGATGTTCTAGTAG 60.676 40.741 0.00 0.00 34.86 2.57
5069 5202 6.092670 GCAGCAAGATTTGTGATGTTCTAGTA 59.907 38.462 0.00 0.00 34.86 1.82
5070 5203 5.106396 GCAGCAAGATTTGTGATGTTCTAGT 60.106 40.000 0.00 0.00 34.86 2.57
5113 5246 1.664965 AGCAACGCGAGAGGAACAC 60.665 57.895 15.93 0.00 0.00 3.32
5118 5251 2.049156 TGACAGCAACGCGAGAGG 60.049 61.111 15.93 0.00 0.00 3.69
5167 5337 3.625313 GGCAGTTATCTTTTGCTCTCTCC 59.375 47.826 0.00 0.00 37.93 3.71
5275 5447 4.689345 GGTTACAGGTAACAACAGCTACAG 59.311 45.833 20.35 0.00 45.32 2.74
5276 5448 4.101274 TGGTTACAGGTAACAACAGCTACA 59.899 41.667 20.35 6.98 45.32 2.74
5277 5449 4.634199 TGGTTACAGGTAACAACAGCTAC 58.366 43.478 20.35 4.87 45.32 3.58
5278 5450 4.959560 TGGTTACAGGTAACAACAGCTA 57.040 40.909 20.35 0.00 45.32 3.32
5279 5451 3.849563 TGGTTACAGGTAACAACAGCT 57.150 42.857 20.35 0.00 45.32 4.24
5280 5452 5.009210 TCAAATGGTTACAGGTAACAACAGC 59.991 40.000 20.35 6.61 45.32 4.40
5420 5611 4.327898 GTGATAGGCAATGCACAAATGTTG 59.672 41.667 7.79 0.00 0.00 3.33
5421 5612 4.497300 GTGATAGGCAATGCACAAATGTT 58.503 39.130 7.79 0.00 0.00 2.71
5422 5613 3.119029 GGTGATAGGCAATGCACAAATGT 60.119 43.478 7.79 0.00 33.09 2.71
5512 5706 2.046411 CTGCACCACCCACGCATA 60.046 61.111 0.00 0.00 34.63 3.14
5572 5770 7.767659 CCTGTCTTTCATAAATCTGATGAGACA 59.232 37.037 14.59 14.59 41.43 3.41
5588 5786 2.494059 CTTTCCGAAGCCTGTCTTTCA 58.506 47.619 0.00 0.00 34.56 2.69
5613 5813 6.837568 ACCCCTAGTCGTCAAGAATAATTCTA 59.162 38.462 0.00 0.00 39.61 2.10
5620 5820 2.904434 ACAACCCCTAGTCGTCAAGAAT 59.096 45.455 0.00 0.00 0.00 2.40
5655 5855 0.475828 ACCTAACCCACAGCTCCCTT 60.476 55.000 0.00 0.00 0.00 3.95
5656 5856 1.161113 ACCTAACCCACAGCTCCCT 59.839 57.895 0.00 0.00 0.00 4.20
5657 5857 1.198759 TCACCTAACCCACAGCTCCC 61.199 60.000 0.00 0.00 0.00 4.30
5658 5858 0.250513 CTCACCTAACCCACAGCTCC 59.749 60.000 0.00 0.00 0.00 4.70
5678 5878 4.954118 ACCAGACACGCCCCCTCA 62.954 66.667 0.00 0.00 0.00 3.86
5679 5879 4.394712 CACCAGACACGCCCCCTC 62.395 72.222 0.00 0.00 0.00 4.30
5764 5964 4.748277 AGCGGTAGAGGTAAATTTAGCA 57.252 40.909 24.95 6.08 33.76 3.49
5777 5977 2.753452 CCAGACAAGACTTAGCGGTAGA 59.247 50.000 0.00 0.00 0.00 2.59
5793 5993 2.079925 GGTGAGTGAATGAAGCCAGAC 58.920 52.381 0.00 0.00 0.00 3.51
5805 6005 2.842462 AGGTGCCGTGGTGAGTGA 60.842 61.111 0.00 0.00 0.00 3.41
5806 6006 2.666190 CAGGTGCCGTGGTGAGTG 60.666 66.667 0.00 0.00 0.00 3.51
5807 6007 4.626081 GCAGGTGCCGTGGTGAGT 62.626 66.667 0.00 0.00 34.31 3.41
5808 6008 2.942796 TAGCAGGTGCCGTGGTGAG 61.943 63.158 0.00 0.00 43.38 3.51
5842 6042 4.347360 AGGATCGATGCTTCATCATCAA 57.653 40.909 14.37 0.00 42.15 2.57


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

AutoCloner maintained by Alex Coulton.