Multiple sequence alignment - TraesCS3D01G544800

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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 TraesCS3D01G544800 chr3D 100.000 6347 0 0 1 6347 614209818 614203472 0.000000e+00 11721.0
1 TraesCS3D01G544800 chr3D 82.558 430 39 10 2 428 614240267 614239871 4.710000e-91 346.0
2 TraesCS3D01G544800 chr3D 77.626 219 26 10 1230 1447 97985776 97985580 1.870000e-20 111.0
3 TraesCS3D01G544800 chr3A 94.169 2967 104 16 1991 4954 750508170 750505270 0.000000e+00 4457.0
4 TraesCS3D01G544800 chr3A 97.496 1358 18 4 4950 6298 750505176 750503826 0.000000e+00 2305.0
5 TraesCS3D01G544800 chr3A 86.068 768 89 12 3 761 750512123 750511365 0.000000e+00 809.0
6 TraesCS3D01G544800 chr3A 78.960 1212 117 57 840 2000 750509316 750508192 0.000000e+00 699.0
7 TraesCS3D01G544800 chr3A 85.358 642 66 13 10 646 750510060 750509442 1.930000e-179 640.0
8 TraesCS3D01G544800 chr3A 79.894 378 55 12 2032 2402 125400285 125399922 2.270000e-64 257.0
9 TraesCS3D01G544800 chr3A 85.081 248 31 5 2032 2277 705928395 705928152 1.370000e-61 248.0
10 TraesCS3D01G544800 chr3A 87.574 169 16 1 882 1045 748208020 748208188 2.340000e-44 191.0
11 TraesCS3D01G544800 chr3A 87.574 169 16 1 882 1045 748550754 748550922 2.340000e-44 191.0
12 TraesCS3D01G544800 chr3A 87.574 169 16 1 882 1045 748664268 748664436 2.340000e-44 191.0
13 TraesCS3D01G544800 chr3A 86.982 169 17 1 882 1045 748459531 748459699 1.090000e-42 185.0
14 TraesCS3D01G544800 chr3A 86.982 169 17 1 882 1045 748743733 748743901 1.090000e-42 185.0
15 TraesCS3D01G544800 chr3A 98.113 53 1 0 6295 6347 750503798 750503746 6.780000e-15 93.5
16 TraesCS3D01G544800 chr3A 92.308 52 4 0 4156 4207 387281500 387281551 2.450000e-09 75.0
17 TraesCS3D01G544800 chr3B 94.670 863 27 7 2414 3274 823581540 823580695 0.000000e+00 1321.0
18 TraesCS3D01G544800 chr3B 89.696 1087 22 24 4950 6016 823578840 823577824 0.000000e+00 1304.0
19 TraesCS3D01G544800 chr3B 90.329 972 33 17 4013 4952 823579863 823578921 0.000000e+00 1218.0
20 TraesCS3D01G544800 chr3B 87.984 749 63 12 20 761 823584446 823583718 0.000000e+00 859.0
21 TraesCS3D01G544800 chr3B 85.286 768 66 26 3273 4007 823580656 823579903 0.000000e+00 749.0
22 TraesCS3D01G544800 chr3B 93.750 416 20 3 1991 2400 823581936 823581521 2.510000e-173 619.0
23 TraesCS3D01G544800 chr3B 80.988 810 64 32 1230 1993 823582730 823581965 1.550000e-155 560.0
24 TraesCS3D01G544800 chr3B 84.680 359 50 4 2033 2389 704306049 704306404 2.810000e-93 353.0
25 TraesCS3D01G544800 chr3B 87.550 249 5 7 6056 6298 823577819 823577591 1.360000e-66 265.0
26 TraesCS3D01G544800 chr3B 79.487 234 25 12 820 1045 823583160 823582942 1.840000e-30 145.0
27 TraesCS3D01G544800 chr3B 98.113 53 1 0 6295 6347 823577566 823577514 6.780000e-15 93.5
28 TraesCS3D01G544800 chr3B 85.507 69 5 1 4581 4644 746342187 746342119 4.110000e-07 67.6
29 TraesCS3D01G544800 chr2B 93.622 392 21 2 2014 2401 397907528 397907919 3.300000e-162 582.0
30 TraesCS3D01G544800 chr2B 84.536 194 20 7 1578 1768 683768664 683768478 3.910000e-42 183.0
31 TraesCS3D01G544800 chr2B 89.796 98 10 0 5900 5997 55881137 55881234 6.680000e-25 126.0
32 TraesCS3D01G544800 chr2B 97.500 40 1 0 4613 4652 513468762 513468723 1.140000e-07 69.4
33 TraesCS3D01G544800 chr5B 93.367 392 22 2 2014 2401 587824650 587825041 1.530000e-160 577.0
34 TraesCS3D01G544800 chr5B 95.082 183 9 0 2421 2603 587825025 587825207 8.050000e-74 289.0
35 TraesCS3D01G544800 chr5B 89.655 58 2 4 4615 4670 701152572 701152627 3.170000e-08 71.3
36 TraesCS3D01G544800 chr1B 93.523 386 22 1 2020 2402 37102328 37101943 7.140000e-159 571.0
37 TraesCS3D01G544800 chr1B 94.764 191 8 2 2414 2603 37101964 37101775 4.810000e-76 296.0
38 TraesCS3D01G544800 chr1B 91.589 107 8 1 5890 5996 52903636 52903741 5.130000e-31 147.0
39 TraesCS3D01G544800 chr1B 95.000 40 2 0 4613 4652 213904178 213904217 5.310000e-06 63.9
40 TraesCS3D01G544800 chr4A 77.869 488 71 18 2029 2509 176615829 176616286 1.050000e-67 268.0
41 TraesCS3D01G544800 chr4A 97.500 40 1 0 1408 1447 427793378 427793417 1.140000e-07 69.4
42 TraesCS3D01G544800 chrUn 87.574 169 16 1 882 1045 320622058 320622226 2.340000e-44 191.0
43 TraesCS3D01G544800 chrUn 77.523 218 16 12 1230 1447 308666333 308666149 4.050000e-17 100.0
44 TraesCS3D01G544800 chr2A 83.505 194 22 7 1578 1768 710382412 710382226 8.460000e-39 172.0
45 TraesCS3D01G544800 chr2A 82.584 178 21 7 1641 1818 138521583 138521416 1.430000e-31 148.0
46 TraesCS3D01G544800 chr2A 89.691 97 10 0 5900 5996 36628193 36628289 2.400000e-24 124.0
47 TraesCS3D01G544800 chr1D 91.589 107 8 1 5890 5996 34622952 34623057 5.130000e-31 147.0
48 TraesCS3D01G544800 chr1D 95.000 40 2 0 4613 4652 133947979 133948018 5.310000e-06 63.9
49 TraesCS3D01G544800 chr7B 88.000 125 11 2 1694 1818 283103456 283103336 1.840000e-30 145.0
50 TraesCS3D01G544800 chr1A 90.909 99 9 0 5898 5996 32896088 32896186 3.990000e-27 134.0
51 TraesCS3D01G544800 chr6A 88.776 98 11 0 5900 5997 76578628 76578725 3.110000e-23 121.0
52 TraesCS3D01G544800 chr6A 97.500 40 1 0 1408 1447 9090754 9090793 1.140000e-07 69.4
53 TraesCS3D01G544800 chr6A 97.436 39 1 0 4613 4651 604890720 604890758 4.110000e-07 67.6
54 TraesCS3D01G544800 chr2D 88.776 98 11 0 5900 5997 33718817 33718914 3.110000e-23 121.0
55 TraesCS3D01G544800 chr5A 77.232 224 18 13 1224 1447 147101620 147101810 4.050000e-17 100.0
56 TraesCS3D01G544800 chr5A 77.232 224 18 13 1224 1447 147104640 147104830 4.050000e-17 100.0
57 TraesCS3D01G544800 chr7A 74.900 251 36 16 1563 1809 693018687 693018460 8.760000e-14 89.8
58 TraesCS3D01G544800 chr4D 75.217 230 30 14 1224 1447 10611454 10611662 4.080000e-12 84.2
59 TraesCS3D01G544800 chr5D 85.965 57 5 2 4614 4670 327056036 327056089 2.470000e-04 58.4
60 TraesCS3D01G544800 chr5D 83.582 67 6 1 4581 4642 549576646 549576580 2.470000e-04 58.4


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 TraesCS3D01G544800 chr3D 614203472 614209818 6346 True 11721.000000 11721 100.000000 1 6347 1 chr3D.!!$R2 6346
1 TraesCS3D01G544800 chr3A 750503746 750512123 8377 True 1500.583333 4457 90.027333 3 6347 6 chr3A.!!$R3 6344
2 TraesCS3D01G544800 chr3B 823577514 823584446 6932 True 713.350000 1321 88.785300 20 6347 10 chr3B.!!$R2 6327
3 TraesCS3D01G544800 chr5B 587824650 587825207 557 False 433.000000 577 94.224500 2014 2603 2 chr5B.!!$F2 589
4 TraesCS3D01G544800 chr1B 37101775 37102328 553 True 433.500000 571 94.143500 2020 2603 2 chr1B.!!$R1 583

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
445 448 0.036306 CCGGACTTAGGGTTGTGCTT 59.964 55.000 0.00 0.0 0.00 3.91 F
1163 3212 0.106519 CCAATCCCAATCCCTCGCTT 60.107 55.000 0.00 0.0 0.00 4.68 F
1481 3565 0.036164 ACGCTGCTGTATGTTCCCAA 59.964 50.000 0.00 0.0 0.00 4.12 F
1855 3981 1.052124 TGGAGGTACCGGCTTATGGG 61.052 60.000 6.18 0.0 42.61 4.00 F
2778 4944 0.250727 TTGAGAAGGCGACAAAGGGG 60.251 55.000 0.00 0.0 0.00 4.79 F
3831 6068 1.135083 AGCACCGTACTCCGAAATCTG 60.135 52.381 0.00 0.0 39.56 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 3455 0.829333 ACTAGTGAGGATGGCTGCTG 59.171 55.000 0.00 0.00 0.00 4.41 R
2397 4563 1.275010 ACACACACACACACACAGAGA 59.725 47.619 0.00 0.00 0.00 3.10 R
2401 4567 1.275010 AGAGACACACACACACACACA 59.725 47.619 0.00 0.00 0.00 3.72 R
3831 6068 1.566563 CAGAGCTGCACACGTGTTC 59.433 57.895 20.79 15.89 0.00 3.18 R
4596 6873 1.649171 CGCTGTACTAAAGCAGTGACG 59.351 52.381 0.00 0.00 43.58 4.35 R
5661 8088 1.376543 AGAACGCATGCAGAAGGATG 58.623 50.000 19.57 0.50 45.39 3.51 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
57 59 1.312815 ACTGAGCTTTTGTGGAGTGC 58.687 50.000 0.00 0.00 0.00 4.40
96 98 4.142609 AGTCATGCGATCATTACCAAGT 57.857 40.909 0.00 0.00 29.28 3.16
150 152 0.478072 ACTTCATGGTGACCAAGGCA 59.522 50.000 9.06 0.00 36.95 4.75
204 206 9.539825 TGATCTTATAGCAGAAAGAACTTGATC 57.460 33.333 0.00 0.00 35.47 2.92
208 210 3.949132 AGCAGAAAGAACTTGATCCCTC 58.051 45.455 0.00 0.00 0.00 4.30
209 211 3.013219 GCAGAAAGAACTTGATCCCTCC 58.987 50.000 0.00 0.00 0.00 4.30
210 212 3.615155 CAGAAAGAACTTGATCCCTCCC 58.385 50.000 0.00 0.00 0.00 4.30
211 213 3.009473 CAGAAAGAACTTGATCCCTCCCA 59.991 47.826 0.00 0.00 0.00 4.37
221 223 1.694696 GATCCCTCCCACCACTCATAC 59.305 57.143 0.00 0.00 0.00 2.39
269 271 3.806521 AGCAGCTGTTCGTGAATCATATC 59.193 43.478 16.64 0.00 0.00 1.63
322 325 1.575244 TGCGCTAAGTCAGATCATGC 58.425 50.000 9.73 0.00 0.00 4.06
366 369 1.034292 GGCTCTTCCACCATGAAGCC 61.034 60.000 0.00 0.00 41.23 4.35
369 372 1.002134 CTTCCACCATGAAGCCCGT 60.002 57.895 0.00 0.00 35.72 5.28
375 378 0.981183 ACCATGAAGCCCGTGACTTA 59.019 50.000 0.00 0.00 33.60 2.24
389 392 0.614134 GACTTAGGGGTGGAGTCGGT 60.614 60.000 0.00 0.00 31.54 4.69
405 408 3.324170 GGTGACGGTGTGATAGACG 57.676 57.895 0.00 0.00 0.00 4.18
423 426 4.103103 GCCTTTCGGTCGCCTTGC 62.103 66.667 0.00 0.00 0.00 4.01
445 448 0.036306 CCGGACTTAGGGTTGTGCTT 59.964 55.000 0.00 0.00 0.00 3.91
460 465 2.919971 GCTTGGAGCAGAACGAACT 58.080 52.632 0.00 0.00 41.89 3.01
469 474 1.429463 CAGAACGAACTAGTGGGTGC 58.571 55.000 0.00 0.00 0.00 5.01
481 486 1.609210 TGGGTGCGAGACAGATCCA 60.609 57.895 0.00 0.00 0.00 3.41
482 487 0.977627 TGGGTGCGAGACAGATCCAT 60.978 55.000 0.00 0.00 0.00 3.41
498 503 2.759355 TCCATCTTGGATAAGGGACGT 58.241 47.619 0.00 0.00 42.67 4.34
550 559 0.948623 CGCAAATGAGTCGGTGGTGA 60.949 55.000 0.00 0.00 0.00 4.02
566 575 0.674895 GTGAGCAAGGACCGAGCAAT 60.675 55.000 12.74 0.00 0.00 3.56
579 588 2.208431 CGAGCAATGAACTGGGAGATC 58.792 52.381 0.00 0.00 0.00 2.75
587 596 2.567169 TGAACTGGGAGATCGACACATT 59.433 45.455 0.00 0.00 0.00 2.71
588 597 3.767131 TGAACTGGGAGATCGACACATTA 59.233 43.478 0.00 0.00 0.00 1.90
597 606 6.239176 GGGAGATCGACACATTAGAGAGAAAT 60.239 42.308 0.00 0.00 0.00 2.17
610 619 3.051496 AGAGAGAAATGGGATCCAGGAGA 60.051 47.826 15.23 0.00 36.75 3.71
615 624 5.019470 AGAAATGGGATCCAGGAGAAAAAC 58.981 41.667 15.23 0.00 36.75 2.43
616 625 4.402616 AATGGGATCCAGGAGAAAAACA 57.597 40.909 15.23 0.00 36.75 2.83
617 626 3.439857 TGGGATCCAGGAGAAAAACAG 57.560 47.619 15.23 0.00 0.00 3.16
619 628 2.095461 GGATCCAGGAGAAAAACAGGC 58.905 52.381 6.95 0.00 0.00 4.85
654 663 4.374689 AAGAAGAAGGAAAAGGGAGGAC 57.625 45.455 0.00 0.00 0.00 3.85
668 677 0.663568 GAGGACACGACAGAACACCG 60.664 60.000 0.00 0.00 0.00 4.94
716 725 0.767375 TGGAGGCAAGTCTCAAAGCT 59.233 50.000 3.88 0.00 35.58 3.74
719 728 2.941720 GGAGGCAAGTCTCAAAGCTATG 59.058 50.000 3.88 0.00 35.58 2.23
763 2719 1.202348 GAAACCGAGCCAATCCCTTTG 59.798 52.381 0.00 0.00 34.93 2.77
804 2761 2.431601 GCTGCGCTCTGTCGAACT 60.432 61.111 9.73 0.00 0.00 3.01
806 2763 0.526524 GCTGCGCTCTGTCGAACTAT 60.527 55.000 9.73 0.00 0.00 2.12
808 2765 2.263077 CTGCGCTCTGTCGAACTATTT 58.737 47.619 9.73 0.00 0.00 1.40
882 2868 7.068103 TCCACACATCTTGTATGAACACTTTTT 59.932 33.333 0.00 0.00 35.67 1.94
930 2925 6.095377 GTGAAAAAGGATATTTCTGCACAGG 58.905 40.000 0.00 0.00 37.60 4.00
974 2969 2.101750 TCCTCGCTCTGTTTGTTGTACA 59.898 45.455 0.00 0.00 0.00 2.90
975 2970 2.476619 CCTCGCTCTGTTTGTTGTACAG 59.523 50.000 0.00 0.00 43.41 2.74
979 2983 2.872245 GCTCTGTTTGTTGTACAGCTGA 59.128 45.455 23.35 0.48 42.12 4.26
985 2989 2.620251 TGTTGTACAGCTGAAGCAGT 57.380 45.000 23.35 5.30 45.16 4.40
1084 3133 3.089838 CCATCCCCAAGGTGAGCA 58.910 61.111 0.00 0.00 0.00 4.26
1085 3134 1.383799 CCATCCCCAAGGTGAGCAA 59.616 57.895 0.00 0.00 0.00 3.91
1086 3135 0.682209 CCATCCCCAAGGTGAGCAAG 60.682 60.000 0.00 0.00 0.00 4.01
1087 3136 1.000396 ATCCCCAAGGTGAGCAAGC 60.000 57.895 0.00 0.00 0.00 4.01
1099 3148 1.690893 TGAGCAAGCTATCTGGGCTAG 59.309 52.381 0.00 0.00 39.30 3.42
1113 3162 4.157120 CTAGGGTTCACCGGCCGG 62.157 72.222 42.17 42.17 46.96 6.13
1129 3178 1.540267 GCCGGAAAGGAAGGAAGAAAC 59.460 52.381 5.05 0.00 45.00 2.78
1134 3183 1.541275 AAGGAAGGAAGAAACCCCCA 58.459 50.000 0.00 0.00 0.00 4.96
1135 3184 1.773541 AGGAAGGAAGAAACCCCCAT 58.226 50.000 0.00 0.00 0.00 4.00
1137 3186 2.043115 AGGAAGGAAGAAACCCCCATTC 59.957 50.000 0.00 0.00 0.00 2.67
1141 3190 1.008327 GGAAGAAACCCCCATTCCCAT 59.992 52.381 0.00 0.00 36.08 4.00
1146 3195 1.158963 AACCCCCATTCCCATTCCCA 61.159 55.000 0.00 0.00 0.00 4.37
1147 3196 1.158963 ACCCCCATTCCCATTCCCAA 61.159 55.000 0.00 0.00 0.00 4.12
1148 3197 0.268566 CCCCCATTCCCATTCCCAAT 59.731 55.000 0.00 0.00 0.00 3.16
1152 3201 1.062275 CCATTCCCATTCCCAATCCCA 60.062 52.381 0.00 0.00 0.00 4.37
1153 3202 2.629098 CCATTCCCATTCCCAATCCCAA 60.629 50.000 0.00 0.00 0.00 4.12
1154 3203 3.320129 CATTCCCATTCCCAATCCCAAT 58.680 45.455 0.00 0.00 0.00 3.16
1156 3205 1.220236 TCCCATTCCCAATCCCAATCC 59.780 52.381 0.00 0.00 0.00 3.01
1157 3206 1.720781 CCATTCCCAATCCCAATCCC 58.279 55.000 0.00 0.00 0.00 3.85
1158 3207 1.221265 CCATTCCCAATCCCAATCCCT 59.779 52.381 0.00 0.00 0.00 4.20
1159 3208 2.601905 CATTCCCAATCCCAATCCCTC 58.398 52.381 0.00 0.00 0.00 4.30
1162 3211 1.533711 CCAATCCCAATCCCTCGCT 59.466 57.895 0.00 0.00 0.00 4.93
1163 3212 0.106519 CCAATCCCAATCCCTCGCTT 60.107 55.000 0.00 0.00 0.00 4.68
1167 3232 2.193248 CCAATCCCTCGCTTCCCC 59.807 66.667 0.00 0.00 0.00 4.81
1168 3233 2.203070 CAATCCCTCGCTTCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
1179 3244 4.676951 TTCCCCGCCCCTTTGCTG 62.677 66.667 0.00 0.00 0.00 4.41
1186 3251 1.678970 GCCCCTTTGCTGACCGAAT 60.679 57.895 0.00 0.00 0.00 3.34
1187 3252 1.657751 GCCCCTTTGCTGACCGAATC 61.658 60.000 0.00 0.00 0.00 2.52
1188 3253 1.369091 CCCCTTTGCTGACCGAATCG 61.369 60.000 0.00 0.00 0.00 3.34
1189 3254 0.391130 CCCTTTGCTGACCGAATCGA 60.391 55.000 3.36 0.00 0.00 3.59
1190 3255 1.438651 CCTTTGCTGACCGAATCGAA 58.561 50.000 3.36 0.00 0.00 3.71
1191 3256 2.009774 CCTTTGCTGACCGAATCGAAT 58.990 47.619 3.36 0.00 0.00 3.34
1192 3257 2.223112 CCTTTGCTGACCGAATCGAATG 60.223 50.000 3.36 0.00 0.00 2.67
1193 3258 0.726827 TTGCTGACCGAATCGAATGC 59.273 50.000 3.36 3.67 0.00 3.56
1195 3260 1.927210 CTGACCGAATCGAATGCCG 59.073 57.895 3.36 0.00 40.25 5.69
1197 3262 2.125310 ACCGAATCGAATGCCGCA 60.125 55.556 3.36 0.00 38.37 5.69
1198 3263 1.498865 GACCGAATCGAATGCCGCAT 61.499 55.000 3.36 0.00 38.37 4.73
1211 3280 2.821366 CGCATGCAGGTGGAGGAC 60.821 66.667 19.57 0.00 0.00 3.85
1214 3283 1.153489 CATGCAGGTGGAGGACGAG 60.153 63.158 0.00 0.00 0.00 4.18
1215 3284 3.023949 ATGCAGGTGGAGGACGAGC 62.024 63.158 0.00 0.00 0.00 5.03
1216 3285 4.459089 GCAGGTGGAGGACGAGCC 62.459 72.222 0.00 0.00 0.00 4.70
1217 3286 3.775654 CAGGTGGAGGACGAGCCC 61.776 72.222 0.00 0.00 37.37 5.19
1218 3287 3.999285 AGGTGGAGGACGAGCCCT 61.999 66.667 0.00 0.00 39.77 5.19
1219 3288 3.775654 GGTGGAGGACGAGCCCTG 61.776 72.222 0.00 0.00 36.49 4.45
1220 3289 4.459089 GTGGAGGACGAGCCCTGC 62.459 72.222 7.54 7.54 43.95 4.85
1221 3290 4.704103 TGGAGGACGAGCCCTGCT 62.704 66.667 13.39 0.00 44.01 4.24
1222 3291 4.154347 GGAGGACGAGCCCTGCTG 62.154 72.222 0.00 0.00 39.88 4.41
1315 3393 2.463441 CCTTGGGAAGGTCAGGTCA 58.537 57.895 0.00 0.00 43.95 4.02
1316 3394 0.771127 CCTTGGGAAGGTCAGGTCAA 59.229 55.000 0.00 0.00 43.95 3.18
1317 3395 1.355720 CCTTGGGAAGGTCAGGTCAAT 59.644 52.381 0.00 0.00 43.95 2.57
1318 3396 2.619074 CCTTGGGAAGGTCAGGTCAATC 60.619 54.545 0.00 0.00 43.95 2.67
1319 3397 2.044793 TGGGAAGGTCAGGTCAATCT 57.955 50.000 0.00 0.00 0.00 2.40
1320 3398 1.909302 TGGGAAGGTCAGGTCAATCTC 59.091 52.381 0.00 0.00 0.00 2.75
1321 3399 1.134670 GGGAAGGTCAGGTCAATCTCG 60.135 57.143 0.00 0.00 0.00 4.04
1322 3400 1.646189 GAAGGTCAGGTCAATCTCGC 58.354 55.000 0.00 0.00 0.00 5.03
1323 3401 1.205893 GAAGGTCAGGTCAATCTCGCT 59.794 52.381 0.00 0.00 0.00 4.93
1324 3402 0.820871 AGGTCAGGTCAATCTCGCTC 59.179 55.000 0.00 0.00 0.00 5.03
1325 3403 0.820871 GGTCAGGTCAATCTCGCTCT 59.179 55.000 0.00 0.00 0.00 4.09
1326 3404 1.205893 GGTCAGGTCAATCTCGCTCTT 59.794 52.381 0.00 0.00 0.00 2.85
1327 3405 2.535331 GTCAGGTCAATCTCGCTCTTC 58.465 52.381 0.00 0.00 0.00 2.87
1328 3406 2.165437 GTCAGGTCAATCTCGCTCTTCT 59.835 50.000 0.00 0.00 0.00 2.85
1329 3407 2.828520 TCAGGTCAATCTCGCTCTTCTT 59.171 45.455 0.00 0.00 0.00 2.52
1330 3408 2.928757 CAGGTCAATCTCGCTCTTCTTG 59.071 50.000 0.00 0.00 0.00 3.02
1331 3409 2.564947 AGGTCAATCTCGCTCTTCTTGT 59.435 45.455 0.00 0.00 0.00 3.16
1332 3410 3.007398 AGGTCAATCTCGCTCTTCTTGTT 59.993 43.478 0.00 0.00 0.00 2.83
1371 3455 2.903284 GCATAGAGCAGAGCAGAGC 58.097 57.895 0.00 0.00 44.79 4.09
1372 3456 0.104487 GCATAGAGCAGAGCAGAGCA 59.896 55.000 0.00 0.00 44.79 4.26
1375 3459 0.969409 TAGAGCAGAGCAGAGCAGCA 60.969 55.000 0.00 0.00 36.85 4.41
1377 3461 3.501548 GCAGAGCAGAGCAGCAGC 61.502 66.667 0.00 0.00 42.56 5.25
1379 3463 3.320014 AGAGCAGAGCAGCAGCCA 61.320 61.111 0.00 0.00 43.56 4.75
1380 3464 2.124653 GAGCAGAGCAGCAGCCAT 60.125 61.111 0.00 0.00 43.56 4.40
1381 3465 2.124653 AGCAGAGCAGCAGCCATC 60.125 61.111 0.00 0.00 43.56 3.51
1382 3466 3.210528 GCAGAGCAGCAGCCATCC 61.211 66.667 0.00 0.00 43.56 3.51
1383 3467 2.590645 CAGAGCAGCAGCCATCCT 59.409 61.111 0.00 0.00 43.56 3.24
1384 3468 1.524165 CAGAGCAGCAGCCATCCTC 60.524 63.158 0.00 0.00 43.56 3.71
1385 3469 1.993948 AGAGCAGCAGCCATCCTCA 60.994 57.895 0.00 0.00 43.56 3.86
1386 3470 1.818785 GAGCAGCAGCCATCCTCAC 60.819 63.158 0.00 0.00 43.56 3.51
1388 3472 0.979709 AGCAGCAGCCATCCTCACTA 60.980 55.000 0.00 0.00 43.56 2.74
1389 3473 0.532417 GCAGCAGCCATCCTCACTAG 60.532 60.000 0.00 0.00 33.58 2.57
1390 3474 0.829333 CAGCAGCCATCCTCACTAGT 59.171 55.000 0.00 0.00 0.00 2.57
1391 3475 2.034878 CAGCAGCCATCCTCACTAGTA 58.965 52.381 0.00 0.00 0.00 1.82
1392 3476 2.432146 CAGCAGCCATCCTCACTAGTAA 59.568 50.000 0.00 0.00 0.00 2.24
1393 3477 2.432510 AGCAGCCATCCTCACTAGTAAC 59.567 50.000 0.00 0.00 0.00 2.50
1394 3478 2.168521 GCAGCCATCCTCACTAGTAACA 59.831 50.000 0.00 0.00 0.00 2.41
1395 3479 3.739519 GCAGCCATCCTCACTAGTAACAG 60.740 52.174 0.00 0.00 0.00 3.16
1406 3490 4.818005 TCACTAGTAACAGTGTTCGTCAGA 59.182 41.667 12.82 2.55 45.11 3.27
1464 3548 0.723414 CATACTGCAACTGCCTCACG 59.277 55.000 0.00 0.00 41.18 4.35
1479 3563 0.391130 TCACGCTGCTGTATGTTCCC 60.391 55.000 0.00 0.00 0.00 3.97
1480 3564 0.673333 CACGCTGCTGTATGTTCCCA 60.673 55.000 0.00 0.00 0.00 4.37
1481 3565 0.036164 ACGCTGCTGTATGTTCCCAA 59.964 50.000 0.00 0.00 0.00 4.12
1482 3566 1.340017 ACGCTGCTGTATGTTCCCAAT 60.340 47.619 0.00 0.00 0.00 3.16
1483 3567 1.745087 CGCTGCTGTATGTTCCCAATT 59.255 47.619 0.00 0.00 0.00 2.32
1486 3570 4.199310 GCTGCTGTATGTTCCCAATTCTA 58.801 43.478 0.00 0.00 0.00 2.10
1488 3572 5.220931 GCTGCTGTATGTTCCCAATTCTAAG 60.221 44.000 0.00 0.00 0.00 2.18
1490 3574 4.640201 GCTGTATGTTCCCAATTCTAAGCA 59.360 41.667 0.00 0.00 0.00 3.91
1491 3575 5.125417 GCTGTATGTTCCCAATTCTAAGCAA 59.875 40.000 0.00 0.00 0.00 3.91
1500 3584 4.829492 CCCAATTCTAAGCAATCCCCTTAG 59.171 45.833 0.00 0.00 41.86 2.18
1554 3638 6.166279 CAGTATCCTGCAACTTTCTTCACTA 58.834 40.000 0.00 0.00 0.00 2.74
1561 3645 6.650807 CCTGCAACTTTCTTCACTACAAGATA 59.349 38.462 0.00 0.00 32.32 1.98
1565 3649 7.171678 GCAACTTTCTTCACTACAAGATACAGT 59.828 37.037 0.00 0.00 32.32 3.55
1573 3657 5.302059 TCACTACAAGATACAGTATCCTGCC 59.698 44.000 16.32 0.00 42.81 4.85
1578 3662 7.136822 ACAAGATACAGTATCCTGCCAATTA 57.863 36.000 16.32 0.00 42.81 1.40
1579 3663 7.573710 ACAAGATACAGTATCCTGCCAATTAA 58.426 34.615 16.32 0.00 42.81 1.40
1580 3664 8.220559 ACAAGATACAGTATCCTGCCAATTAAT 58.779 33.333 16.32 0.00 42.81 1.40
1581 3665 9.071276 CAAGATACAGTATCCTGCCAATTAATT 57.929 33.333 15.87 0.00 42.81 1.40
1583 3667 9.646522 AGATACAGTATCCTGCCAATTAATTTT 57.353 29.630 15.87 0.00 42.81 1.82
1589 3673 9.212593 AGTATCCTGCCAATTAATTTTTATGGT 57.787 29.630 0.00 0.00 33.63 3.55
1593 3677 7.120432 TCCTGCCAATTAATTTTTATGGTTTGC 59.880 33.333 0.00 0.00 33.63 3.68
1632 3716 4.889832 AATATGCAGCAGCTTACTCAAC 57.110 40.909 0.00 0.00 42.74 3.18
1687 3777 3.260483 CGATGCTGTCGCCAGAGC 61.260 66.667 0.00 0.00 44.33 4.09
1787 3905 2.850254 GCTTGCCGCATTTGTTTGTTTG 60.850 45.455 0.00 0.00 38.92 2.93
1808 3926 7.122650 TGTTTGTTCTGAAAGATTTCTCCTTGT 59.877 33.333 6.84 0.00 46.36 3.16
1855 3981 1.052124 TGGAGGTACCGGCTTATGGG 61.052 60.000 6.18 0.00 42.61 4.00
1863 3989 1.510844 CGGCTTATGGGTGTTTGCC 59.489 57.895 0.00 0.00 37.24 4.52
1933 4059 3.313526 GGATCAGATGCACAACATGGTAC 59.686 47.826 0.00 0.00 39.84 3.34
2148 4311 7.376335 AGGGGAATCCAAGTATAGTTCTTAC 57.624 40.000 0.09 0.00 38.24 2.34
2149 4312 6.906901 AGGGGAATCCAAGTATAGTTCTTACA 59.093 38.462 0.09 0.00 38.24 2.41
2226 4389 5.892686 TGAGCCCATGAATTATCACATTTGA 59.107 36.000 0.00 0.00 38.69 2.69
2252 4418 5.717119 ACTGAAAATATTTGAGGCAGCAAG 58.283 37.500 0.39 0.00 0.00 4.01
2265 4431 4.202441 AGGCAGCAAGTATGTAATTCCTG 58.798 43.478 0.00 0.00 0.00 3.86
2396 4562 3.367292 CCAGTTTGTGCTCTCTCTCTCTC 60.367 52.174 0.00 0.00 0.00 3.20
2397 4563 3.507233 CAGTTTGTGCTCTCTCTCTCTCT 59.493 47.826 0.00 0.00 0.00 3.10
2398 4564 3.758554 AGTTTGTGCTCTCTCTCTCTCTC 59.241 47.826 0.00 0.00 0.00 3.20
2399 4565 3.719268 TTGTGCTCTCTCTCTCTCTCT 57.281 47.619 0.00 0.00 0.00 3.10
2400 4566 3.266510 TGTGCTCTCTCTCTCTCTCTC 57.733 52.381 0.00 0.00 0.00 3.20
2401 4567 2.840038 TGTGCTCTCTCTCTCTCTCTCT 59.160 50.000 0.00 0.00 0.00 3.10
2402 4568 3.201290 GTGCTCTCTCTCTCTCTCTCTG 58.799 54.545 0.00 0.00 0.00 3.35
2403 4569 2.840038 TGCTCTCTCTCTCTCTCTCTGT 59.160 50.000 0.00 0.00 0.00 3.41
2404 4570 3.201290 GCTCTCTCTCTCTCTCTCTGTG 58.799 54.545 0.00 0.00 0.00 3.66
2405 4571 3.369892 GCTCTCTCTCTCTCTCTCTGTGT 60.370 52.174 0.00 0.00 0.00 3.72
2406 4572 4.186926 CTCTCTCTCTCTCTCTCTGTGTG 58.813 52.174 0.00 0.00 0.00 3.82
2407 4573 3.582647 TCTCTCTCTCTCTCTCTGTGTGT 59.417 47.826 0.00 0.00 0.00 3.72
2408 4574 3.673902 TCTCTCTCTCTCTCTGTGTGTG 58.326 50.000 0.00 0.00 0.00 3.82
2409 4575 3.072330 TCTCTCTCTCTCTCTGTGTGTGT 59.928 47.826 0.00 0.00 0.00 3.72
2410 4576 3.145286 TCTCTCTCTCTCTGTGTGTGTG 58.855 50.000 0.00 0.00 0.00 3.82
2411 4577 2.884012 CTCTCTCTCTCTGTGTGTGTGT 59.116 50.000 0.00 0.00 0.00 3.72
2412 4578 2.620585 TCTCTCTCTCTGTGTGTGTGTG 59.379 50.000 0.00 0.00 0.00 3.82
2413 4579 2.360483 CTCTCTCTCTGTGTGTGTGTGT 59.640 50.000 0.00 0.00 0.00 3.72
2414 4580 2.099756 TCTCTCTCTGTGTGTGTGTGTG 59.900 50.000 0.00 0.00 0.00 3.82
2415 4581 1.824852 TCTCTCTGTGTGTGTGTGTGT 59.175 47.619 0.00 0.00 0.00 3.72
2416 4582 1.929169 CTCTCTGTGTGTGTGTGTGTG 59.071 52.381 0.00 0.00 0.00 3.82
2428 4594 2.620585 TGTGTGTGTGTCTCTCTCTCTG 59.379 50.000 0.00 0.00 0.00 3.35
2532 4698 5.231991 CGTTTTCCACATTTGTTTGGAGAAG 59.768 40.000 0.00 0.00 42.93 2.85
2644 4810 8.484214 ACTAAATGATATCTTGGTAGCTGAGA 57.516 34.615 3.98 0.00 0.00 3.27
2741 4907 6.801539 TGACACAGTTGTATGATCCTTTTC 57.198 37.500 0.00 0.00 35.47 2.29
2778 4944 0.250727 TTGAGAAGGCGACAAAGGGG 60.251 55.000 0.00 0.00 0.00 4.79
3145 5312 9.489084 GGCACTTTACTTATTTTCCATTCTTTT 57.511 29.630 0.00 0.00 0.00 2.27
3242 5410 4.398044 GTGAACAGGTGAGTTTTGGAGAAA 59.602 41.667 0.00 0.00 0.00 2.52
3310 5518 3.981071 AAATGTCTCTGGGAATGACGA 57.019 42.857 0.00 0.00 33.81 4.20
3448 5662 5.905331 TCCAGAAACATATATGACCAGGTCT 59.095 40.000 20.82 8.75 33.15 3.85
3529 5761 4.425577 AATGAAGCATCGGAACTTGTTC 57.574 40.909 5.03 5.03 0.00 3.18
3695 5928 1.805254 CTCTTGAAGCATTGCCCCG 59.195 57.895 4.70 0.00 0.00 5.73
3764 5998 9.812347 TTTCAGGCACATATTTGGATAGATATT 57.188 29.630 0.00 0.00 0.00 1.28
3831 6068 1.135083 AGCACCGTACTCCGAAATCTG 60.135 52.381 0.00 0.00 39.56 2.90
3837 6074 2.592897 CGTACTCCGAAATCTGAACACG 59.407 50.000 0.00 0.00 39.56 4.49
3864 6101 1.478510 GCTCTGGCTGCACTAGAACTA 59.521 52.381 0.50 0.00 35.15 2.24
4122 6397 1.953686 TGTTTCAGGCCAGCTTTGTAC 59.046 47.619 5.01 0.00 0.00 2.90
4128 6404 2.030805 CAGGCCAGCTTTGTACTGTTTC 60.031 50.000 5.01 0.00 33.09 2.78
4132 6408 3.066760 GCCAGCTTTGTACTGTTTCTGTT 59.933 43.478 0.00 0.00 33.09 3.16
4190 6466 3.005155 AGTTTCTTGAAATCCAGCAGTGC 59.995 43.478 7.13 7.13 0.00 4.40
4429 6706 2.701951 TGCATGATGAGAGCATGGTCTA 59.298 45.455 26.54 12.24 42.53 2.59
4446 6723 5.056480 TGGTCTATGTTTTGTGTCACTGAG 58.944 41.667 4.27 0.00 0.00 3.35
4600 6877 7.827236 ACTTTTTCCCATTCATATTACTCGTCA 59.173 33.333 0.00 0.00 0.00 4.35
4605 6882 5.292765 CCATTCATATTACTCGTCACTGCT 58.707 41.667 0.00 0.00 0.00 4.24
4703 7007 6.638096 TCATTCAGTGACACAACAATGATT 57.362 33.333 16.79 4.07 42.73 2.57
5240 7653 2.180432 GCATCTAGGAGCATGCATCA 57.820 50.000 21.98 0.52 44.18 3.07
5381 7801 7.536895 CTAATTATAGGAGCATGCATGAGAC 57.463 40.000 30.64 17.40 0.00 3.36
5493 7920 3.996363 TGTGTAGTGTGCTGCTAGAAATG 59.004 43.478 0.00 0.00 0.00 2.32
5508 7935 6.015519 TGCTAGAAATGTTAGGCATGTTTGTT 60.016 34.615 0.00 0.00 37.96 2.83
5543 7970 7.065120 TGACATGATTTTTGGAGGTTTGATT 57.935 32.000 0.00 0.00 0.00 2.57
5586 8013 0.542467 TTCAACAGCCCCATGCATGT 60.542 50.000 24.58 4.09 44.83 3.21
5661 8088 1.808945 CCATCACTTCCACTGCACTTC 59.191 52.381 0.00 0.00 0.00 3.01
5783 8211 0.253207 TCCTCCCTCCCCCTTTCTTC 60.253 60.000 0.00 0.00 0.00 2.87
6298 8736 6.013725 TGGTACTTGATCAGTGTTAGTTCCAT 60.014 38.462 15.16 0.00 35.97 3.41
6300 8738 7.064728 GGTACTTGATCAGTGTTAGTTCCATTC 59.935 40.741 12.71 0.00 35.97 2.67
6301 8739 6.773638 ACTTGATCAGTGTTAGTTCCATTCT 58.226 36.000 0.00 0.00 32.83 2.40
6303 8741 6.114187 TGATCAGTGTTAGTTCCATTCTGT 57.886 37.500 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 37 3.699067 CACTCCACAAAAGCTCAGTTTG 58.301 45.455 7.64 7.64 40.95 2.93
57 59 2.812591 GACTTGCCTGGCATATCTCATG 59.187 50.000 24.03 7.85 38.76 3.07
96 98 3.500331 TCGAGGTATAGGCCGACAA 57.500 52.632 0.00 0.00 0.00 3.18
150 152 5.510430 GGAGAAACCTTGGGATTCTAATGT 58.490 41.667 8.67 0.00 43.28 2.71
204 206 0.686441 TCGTATGAGTGGTGGGAGGG 60.686 60.000 0.00 0.00 0.00 4.30
208 210 1.670811 GCAATTCGTATGAGTGGTGGG 59.329 52.381 1.25 0.00 0.00 4.61
209 211 2.632377 AGCAATTCGTATGAGTGGTGG 58.368 47.619 2.58 0.00 0.00 4.61
210 212 3.684305 TGAAGCAATTCGTATGAGTGGTG 59.316 43.478 3.88 0.00 0.00 4.17
211 213 3.937814 TGAAGCAATTCGTATGAGTGGT 58.062 40.909 0.00 0.00 0.00 4.16
221 223 3.369546 AAGGTGGTTTGAAGCAATTCG 57.630 42.857 0.00 0.00 38.25 3.34
269 271 3.125316 GTCGGCTACTCCATTTTTGTCTG 59.875 47.826 0.00 0.00 34.01 3.51
322 325 0.107508 AGGATGTCGTGATGCAAGGG 60.108 55.000 0.00 0.00 0.00 3.95
329 332 0.833287 CCTTGGGAGGATGTCGTGAT 59.167 55.000 0.00 0.00 46.74 3.06
330 333 1.899437 GCCTTGGGAGGATGTCGTGA 61.899 60.000 0.00 0.00 46.74 4.35
366 369 0.903454 ACTCCACCCCTAAGTCACGG 60.903 60.000 0.00 0.00 0.00 4.94
369 372 0.613853 CCGACTCCACCCCTAAGTCA 60.614 60.000 0.00 0.00 39.49 3.41
375 378 2.603776 GTCACCGACTCCACCCCT 60.604 66.667 0.00 0.00 0.00 4.79
379 382 2.049433 CACCGTCACCGACTCCAC 60.049 66.667 0.00 0.00 35.63 4.02
389 392 1.509463 GCCGTCTATCACACCGTCA 59.491 57.895 0.00 0.00 0.00 4.35
423 426 0.321298 CACAACCCTAAGTCCGGTGG 60.321 60.000 0.00 0.00 30.96 4.61
445 448 1.272490 CCACTAGTTCGTTCTGCTCCA 59.728 52.381 0.00 0.00 0.00 3.86
460 465 1.103803 GATCTGTCTCGCACCCACTA 58.896 55.000 0.00 0.00 0.00 2.74
481 486 1.687123 CCGACGTCCCTTATCCAAGAT 59.313 52.381 10.58 0.00 33.20 2.40
482 487 1.108776 CCGACGTCCCTTATCCAAGA 58.891 55.000 10.58 0.00 33.20 3.02
550 559 0.036732 TTCATTGCTCGGTCCTTGCT 59.963 50.000 4.90 0.00 0.00 3.91
566 575 1.627864 TGTGTCGATCTCCCAGTTCA 58.372 50.000 0.00 0.00 0.00 3.18
579 588 5.011090 TCCCATTTCTCTCTAATGTGTCG 57.989 43.478 0.00 0.00 32.38 4.35
587 596 4.170845 TCTCCTGGATCCCATTTCTCTCTA 59.829 45.833 9.90 0.00 30.82 2.43
588 597 3.051496 TCTCCTGGATCCCATTTCTCTCT 60.051 47.826 9.90 0.00 30.82 3.10
597 606 2.041620 CCTGTTTTTCTCCTGGATCCCA 59.958 50.000 9.90 0.00 0.00 4.37
610 619 0.698818 ATCTCCTCCCGCCTGTTTTT 59.301 50.000 0.00 0.00 0.00 1.94
615 624 1.274728 CTTATGATCTCCTCCCGCCTG 59.725 57.143 0.00 0.00 0.00 4.85
616 625 1.148027 TCTTATGATCTCCTCCCGCCT 59.852 52.381 0.00 0.00 0.00 5.52
617 626 1.633774 TCTTATGATCTCCTCCCGCC 58.366 55.000 0.00 0.00 0.00 6.13
619 628 4.021544 CCTTCTTCTTATGATCTCCTCCCG 60.022 50.000 0.00 0.00 0.00 5.14
654 663 2.014554 CGACCGGTGTTCTGTCGTG 61.015 63.158 14.63 0.00 33.50 4.35
668 677 2.649614 GGCTATAGTCCGGCGACC 59.350 66.667 9.30 0.00 40.12 4.79
711 720 3.440173 ACGCACAATACTTGCATAGCTTT 59.560 39.130 0.00 0.00 40.20 3.51
716 725 4.000325 ACTTCACGCACAATACTTGCATA 59.000 39.130 0.00 0.00 40.20 3.14
719 728 2.721797 CGACTTCACGCACAATACTTGC 60.722 50.000 0.00 0.00 36.57 4.01
882 2868 8.714179 CACAAGGATAAATTTCTACACACGTTA 58.286 33.333 0.00 0.00 0.00 3.18
906 2894 6.095377 CCTGTGCAGAAATATCCTTTTTCAC 58.905 40.000 0.02 0.00 35.90 3.18
930 2925 1.446272 CCGGAAACAGAGCGAGGAC 60.446 63.158 0.00 0.00 0.00 3.85
974 2969 1.265236 ACTCTGCTACTGCTTCAGCT 58.735 50.000 0.00 0.00 42.66 4.24
975 2970 2.481104 CCTACTCTGCTACTGCTTCAGC 60.481 54.545 0.00 0.00 40.48 4.26
979 2983 2.024846 TCCTCCTACTCTGCTACTGCTT 60.025 50.000 0.00 0.00 40.48 3.91
985 2989 1.819697 CGCCATCCTCCTACTCTGCTA 60.820 57.143 0.00 0.00 0.00 3.49
1060 3094 4.794648 CTTGGGGATGGCGGCGAA 62.795 66.667 12.98 0.00 0.00 4.70
1084 3133 2.050918 GAACCCTAGCCCAGATAGCTT 58.949 52.381 0.00 0.00 41.83 3.74
1085 3134 1.062121 TGAACCCTAGCCCAGATAGCT 60.062 52.381 0.00 0.00 44.49 3.32
1086 3135 1.070914 GTGAACCCTAGCCCAGATAGC 59.929 57.143 0.00 0.00 0.00 2.97
1087 3136 1.694696 GGTGAACCCTAGCCCAGATAG 59.305 57.143 0.00 0.00 0.00 2.08
1099 3148 4.646877 TTTCCGGCCGGTGAACCC 62.647 66.667 41.57 0.00 36.47 4.11
1113 3162 2.158370 TGGGGGTTTCTTCCTTCCTTTC 60.158 50.000 0.00 0.00 0.00 2.62
1117 3166 2.457598 GAATGGGGGTTTCTTCCTTCC 58.542 52.381 0.00 0.00 0.00 3.46
1118 3167 2.457598 GGAATGGGGGTTTCTTCCTTC 58.542 52.381 0.00 0.00 35.36 3.46
1129 3178 0.268566 ATTGGGAATGGGAATGGGGG 59.731 55.000 0.00 0.00 0.00 5.40
1134 3183 3.590714 GATTGGGATTGGGAATGGGAAT 58.409 45.455 0.00 0.00 0.00 3.01
1135 3184 2.360209 GGATTGGGATTGGGAATGGGAA 60.360 50.000 0.00 0.00 0.00 3.97
1137 3186 1.720781 GGATTGGGATTGGGAATGGG 58.279 55.000 0.00 0.00 0.00 4.00
1141 3190 0.550914 CGAGGGATTGGGATTGGGAA 59.449 55.000 0.00 0.00 0.00 3.97
1146 3195 0.183731 GGAAGCGAGGGATTGGGATT 59.816 55.000 0.00 0.00 0.00 3.01
1147 3196 1.709994 GGGAAGCGAGGGATTGGGAT 61.710 60.000 0.00 0.00 0.00 3.85
1148 3197 2.375345 GGGAAGCGAGGGATTGGGA 61.375 63.158 0.00 0.00 0.00 4.37
1152 3201 4.176752 GCGGGGAAGCGAGGGATT 62.177 66.667 0.00 0.00 0.00 3.01
1162 3211 4.676951 CAGCAAAGGGGCGGGGAA 62.677 66.667 0.00 0.00 39.27 3.97
1167 3232 4.697756 TCGGTCAGCAAAGGGGCG 62.698 66.667 0.00 0.00 39.27 6.13
1168 3233 1.657751 GATTCGGTCAGCAAAGGGGC 61.658 60.000 0.00 0.00 0.00 5.80
1179 3244 1.498865 ATGCGGCATTCGATTCGGTC 61.499 55.000 10.23 0.00 42.43 4.79
1181 3246 1.082561 CATGCGGCATTCGATTCGG 60.083 57.895 13.81 0.00 42.43 4.30
1182 3247 1.723542 GCATGCGGCATTCGATTCG 60.724 57.895 13.81 0.00 43.97 3.34
1183 3248 4.216963 GCATGCGGCATTCGATTC 57.783 55.556 13.81 0.00 43.97 2.52
1193 3258 4.100084 TCCTCCACCTGCATGCGG 62.100 66.667 20.13 20.13 0.00 5.69
1195 3260 2.821366 CGTCCTCCACCTGCATGC 60.821 66.667 11.82 11.82 0.00 4.06
1197 3262 3.023949 GCTCGTCCTCCACCTGCAT 62.024 63.158 0.00 0.00 0.00 3.96
1198 3263 3.695606 GCTCGTCCTCCACCTGCA 61.696 66.667 0.00 0.00 0.00 4.41
1206 3275 4.828925 GCAGCAGGGCTCGTCCTC 62.829 72.222 0.00 0.00 36.40 3.71
1217 3286 4.351054 AGGAAACCCCCGCAGCAG 62.351 66.667 0.00 0.00 34.66 4.24
1218 3287 4.344865 GAGGAAACCCCCGCAGCA 62.345 66.667 0.00 0.00 34.66 4.41
1220 3289 4.426313 GGGAGGAAACCCCCGCAG 62.426 72.222 0.00 0.00 43.81 5.18
1228 3306 2.361737 GCAGCCAGGGGAGGAAAC 60.362 66.667 0.00 0.00 0.00 2.78
1263 3341 4.862092 CAGCGCCGACGAGATGCT 62.862 66.667 2.29 0.00 43.93 3.79
1289 3367 2.757077 CTTCCCAAGGGCGAGGTT 59.243 61.111 0.00 0.00 34.68 3.50
1310 3388 2.564947 ACAAGAAGAGCGAGATTGACCT 59.435 45.455 0.00 0.00 0.00 3.85
1312 3390 4.999751 AAACAAGAAGAGCGAGATTGAC 57.000 40.909 0.00 0.00 0.00 3.18
1315 3393 3.503748 CCCAAAACAAGAAGAGCGAGATT 59.496 43.478 0.00 0.00 0.00 2.40
1316 3394 3.077359 CCCAAAACAAGAAGAGCGAGAT 58.923 45.455 0.00 0.00 0.00 2.75
1317 3395 2.158813 ACCCAAAACAAGAAGAGCGAGA 60.159 45.455 0.00 0.00 0.00 4.04
1318 3396 2.222027 ACCCAAAACAAGAAGAGCGAG 58.778 47.619 0.00 0.00 0.00 5.03
1319 3397 2.341846 ACCCAAAACAAGAAGAGCGA 57.658 45.000 0.00 0.00 0.00 4.93
1320 3398 3.058914 CAGTACCCAAAACAAGAAGAGCG 60.059 47.826 0.00 0.00 0.00 5.03
1321 3399 3.883489 ACAGTACCCAAAACAAGAAGAGC 59.117 43.478 0.00 0.00 0.00 4.09
1322 3400 4.211374 CGACAGTACCCAAAACAAGAAGAG 59.789 45.833 0.00 0.00 0.00 2.85
1323 3401 4.124238 CGACAGTACCCAAAACAAGAAGA 58.876 43.478 0.00 0.00 0.00 2.87
1324 3402 4.124238 TCGACAGTACCCAAAACAAGAAG 58.876 43.478 0.00 0.00 0.00 2.85
1325 3403 4.139859 TCGACAGTACCCAAAACAAGAA 57.860 40.909 0.00 0.00 0.00 2.52
1326 3404 3.823281 TCGACAGTACCCAAAACAAGA 57.177 42.857 0.00 0.00 0.00 3.02
1327 3405 5.212194 CAAATCGACAGTACCCAAAACAAG 58.788 41.667 0.00 0.00 0.00 3.16
1328 3406 4.498345 GCAAATCGACAGTACCCAAAACAA 60.498 41.667 0.00 0.00 0.00 2.83
1329 3407 3.003897 GCAAATCGACAGTACCCAAAACA 59.996 43.478 0.00 0.00 0.00 2.83
1330 3408 3.252458 AGCAAATCGACAGTACCCAAAAC 59.748 43.478 0.00 0.00 0.00 2.43
1331 3409 3.252215 CAGCAAATCGACAGTACCCAAAA 59.748 43.478 0.00 0.00 0.00 2.44
1332 3410 2.811431 CAGCAAATCGACAGTACCCAAA 59.189 45.455 0.00 0.00 0.00 3.28
1371 3455 0.829333 ACTAGTGAGGATGGCTGCTG 59.171 55.000 0.00 0.00 0.00 4.41
1372 3456 2.432510 GTTACTAGTGAGGATGGCTGCT 59.567 50.000 5.39 0.00 0.00 4.24
1375 3459 3.714144 ACTGTTACTAGTGAGGATGGCT 58.286 45.455 5.39 0.00 0.00 4.75
1385 3469 5.106237 GGATCTGACGAACACTGTTACTAGT 60.106 44.000 0.00 0.00 0.00 2.57
1386 3470 5.124138 AGGATCTGACGAACACTGTTACTAG 59.876 44.000 0.00 0.00 0.00 2.57
1388 3472 3.827302 AGGATCTGACGAACACTGTTACT 59.173 43.478 0.00 0.00 0.00 2.24
1389 3473 4.175787 AGGATCTGACGAACACTGTTAC 57.824 45.455 0.00 0.00 0.00 2.50
1390 3474 4.038763 ACAAGGATCTGACGAACACTGTTA 59.961 41.667 0.00 0.00 0.00 2.41
1391 3475 3.181465 ACAAGGATCTGACGAACACTGTT 60.181 43.478 0.00 0.00 0.00 3.16
1392 3476 2.365617 ACAAGGATCTGACGAACACTGT 59.634 45.455 0.00 0.00 0.00 3.55
1393 3477 3.032017 ACAAGGATCTGACGAACACTG 57.968 47.619 0.00 0.00 0.00 3.66
1394 3478 3.654414 GAACAAGGATCTGACGAACACT 58.346 45.455 0.00 0.00 0.00 3.55
1395 3479 2.408704 CGAACAAGGATCTGACGAACAC 59.591 50.000 0.00 0.00 0.00 3.32
1464 3548 3.019564 AGAATTGGGAACATACAGCAGC 58.980 45.455 0.00 0.00 42.32 5.25
1479 3563 7.410120 AAACTAAGGGGATTGCTTAGAATTG 57.590 36.000 0.00 0.00 35.39 2.32
1480 3564 8.435931 AAAAACTAAGGGGATTGCTTAGAATT 57.564 30.769 0.00 0.00 35.39 2.17
1597 3681 8.131100 GCTGCTGCATATTTACAAGAAGATAAA 58.869 33.333 11.11 0.00 39.41 1.40
1600 3684 5.826737 AGCTGCTGCATATTTACAAGAAGAT 59.173 36.000 18.42 0.00 42.74 2.40
1610 3694 4.701651 TGTTGAGTAAGCTGCTGCATATTT 59.298 37.500 18.42 5.73 42.74 1.40
1614 3698 1.808945 GTGTTGAGTAAGCTGCTGCAT 59.191 47.619 18.42 8.55 42.74 3.96
1632 3716 3.142174 GGACCTCTTGAGGAAGTTTGTG 58.858 50.000 22.10 0.00 0.00 3.33
1787 3905 6.260936 TGACACAAGGAGAAATCTTTCAGAAC 59.739 38.462 5.53 0.00 39.61 3.01
1855 3981 2.161609 CCGATTCCTACAAGGCAAACAC 59.838 50.000 0.00 0.00 34.61 3.32
1863 3989 1.543429 GCCCATCCCGATTCCTACAAG 60.543 57.143 0.00 0.00 0.00 3.16
1933 4059 3.358707 TCCATTGCATAGGTACGTACG 57.641 47.619 18.98 15.01 0.00 3.67
1942 4068 6.798476 CGCTATGTAACATTTCCATTGCATAG 59.202 38.462 14.16 14.16 46.16 2.23
2141 4304 8.888579 ATGGTGCATTACTACTATGTAAGAAC 57.111 34.615 0.00 0.00 36.10 3.01
2226 4389 6.523840 TGCTGCCTCAAATATTTTCAGTTTT 58.476 32.000 0.00 0.00 0.00 2.43
2252 4418 6.017605 CCAGAACATCTGCAGGAATTACATAC 60.018 42.308 15.13 0.00 42.98 2.39
2265 4431 1.487976 TCCAGATCCCAGAACATCTGC 59.512 52.381 1.79 0.00 42.98 4.26
2332 4498 3.926616 TCCTGATTCGTTCCTTCTGTTC 58.073 45.455 0.00 0.00 0.00 3.18
2396 4562 1.929169 CACACACACACACACAGAGAG 59.071 52.381 0.00 0.00 0.00 3.20
2397 4563 1.275010 ACACACACACACACACAGAGA 59.725 47.619 0.00 0.00 0.00 3.10
2398 4564 1.660607 GACACACACACACACACAGAG 59.339 52.381 0.00 0.00 0.00 3.35
2399 4565 1.275010 AGACACACACACACACACAGA 59.725 47.619 0.00 0.00 0.00 3.41
2400 4566 1.660607 GAGACACACACACACACACAG 59.339 52.381 0.00 0.00 0.00 3.66
2401 4567 1.275010 AGAGACACACACACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
2402 4568 1.927174 GAGAGACACACACACACACAC 59.073 52.381 0.00 0.00 0.00 3.82
2403 4569 1.824852 AGAGAGACACACACACACACA 59.175 47.619 0.00 0.00 0.00 3.72
2404 4570 2.099921 AGAGAGAGACACACACACACAC 59.900 50.000 0.00 0.00 0.00 3.82
2405 4571 2.359214 GAGAGAGAGACACACACACACA 59.641 50.000 0.00 0.00 0.00 3.72
2406 4572 2.621055 AGAGAGAGAGACACACACACAC 59.379 50.000 0.00 0.00 0.00 3.82
2407 4573 2.620585 CAGAGAGAGAGACACACACACA 59.379 50.000 0.00 0.00 0.00 3.72
2408 4574 2.621055 ACAGAGAGAGAGACACACACAC 59.379 50.000 0.00 0.00 0.00 3.82
2409 4575 2.881513 GACAGAGAGAGAGACACACACA 59.118 50.000 0.00 0.00 0.00 3.72
2410 4576 3.146066 AGACAGAGAGAGAGACACACAC 58.854 50.000 0.00 0.00 0.00 3.82
2411 4577 3.072330 AGAGACAGAGAGAGAGACACACA 59.928 47.826 0.00 0.00 0.00 3.72
2412 4578 3.674997 AGAGACAGAGAGAGAGACACAC 58.325 50.000 0.00 0.00 0.00 3.82
2413 4579 3.582647 AGAGAGACAGAGAGAGAGACACA 59.417 47.826 0.00 0.00 0.00 3.72
2414 4580 4.184629 GAGAGAGACAGAGAGAGAGACAC 58.815 52.174 0.00 0.00 0.00 3.67
2415 4581 3.837731 TGAGAGAGACAGAGAGAGAGACA 59.162 47.826 0.00 0.00 0.00 3.41
2416 4582 4.471904 TGAGAGAGACAGAGAGAGAGAC 57.528 50.000 0.00 0.00 0.00 3.36
2532 4698 3.507233 TGCATGAAATCCTCCAGTTTGAC 59.493 43.478 0.00 0.00 0.00 3.18
2644 4810 4.787135 AAACCACCCAATTTCCAACATT 57.213 36.364 0.00 0.00 0.00 2.71
2741 4907 9.277565 CCTTCTCAAATAAAATCACACATAACG 57.722 33.333 0.00 0.00 0.00 3.18
3050 5217 5.794894 TGTACCTCTGAAACATCTTTCTCC 58.205 41.667 0.00 0.00 37.30 3.71
3081 5248 5.003804 CACTACTAGGCATTGAACCAAAGT 58.996 41.667 0.00 0.00 32.39 2.66
3145 5312 9.244292 AGAGCAGAGTATTGATCCGTATATAAA 57.756 33.333 0.00 0.00 34.10 1.40
3283 5491 6.012113 TCATTCCCAGAGACATTTTGTGAAT 58.988 36.000 0.00 0.00 0.00 2.57
3369 5583 5.352569 GGCATTCGAGTATTTCCCATATCTG 59.647 44.000 0.00 0.00 0.00 2.90
3448 5662 7.867305 TTGACCATCAAACTGTAGTTTTACA 57.133 32.000 7.25 0.00 45.07 2.41
3529 5761 6.436843 ACCAAGAAGCCATAATTTCTTACG 57.563 37.500 0.00 0.00 40.62 3.18
3545 5777 1.694150 CTGGTGTCAGAGGACCAAGAA 59.306 52.381 0.00 0.00 41.76 2.52
3764 5998 8.862325 TTTTATAAAGTGGATCTTGCTCTGAA 57.138 30.769 0.00 0.00 36.40 3.02
3831 6068 1.566563 CAGAGCTGCACACGTGTTC 59.433 57.895 20.79 15.89 0.00 3.18
3954 6191 7.394359 ACCTTAACTGTCTGATGTTTGCATTAT 59.606 33.333 0.00 0.00 35.07 1.28
3968 6206 4.993705 TTCCATTCCACCTTAACTGTCT 57.006 40.909 0.00 0.00 0.00 3.41
4122 6397 8.365399 TGTAAATCAGTAGACAACAGAAACAG 57.635 34.615 0.00 0.00 0.00 3.16
4128 6404 7.095060 ACTGCATTGTAAATCAGTAGACAACAG 60.095 37.037 0.00 0.00 37.94 3.16
4132 6408 6.463360 TCACTGCATTGTAAATCAGTAGACA 58.537 36.000 3.77 0.00 37.66 3.41
4190 6466 3.734293 GCGCTAGTAAGGTGGACAGTTAG 60.734 52.174 0.00 0.00 0.00 2.34
4429 6706 7.445096 TCATTCATACTCAGTGACACAAAACAT 59.555 33.333 8.59 0.00 0.00 2.71
4446 6723 5.888161 ACTTCCCTGTTTCCATCATTCATAC 59.112 40.000 0.00 0.00 0.00 2.39
4578 6855 6.761242 CAGTGACGAGTAATATGAATGGGAAA 59.239 38.462 0.00 0.00 0.00 3.13
4579 6856 6.280643 CAGTGACGAGTAATATGAATGGGAA 58.719 40.000 0.00 0.00 0.00 3.97
4596 6873 1.649171 CGCTGTACTAAAGCAGTGACG 59.351 52.381 0.00 0.00 43.58 4.35
4600 6877 3.380479 TTGTCGCTGTACTAAAGCAGT 57.620 42.857 4.74 0.00 40.86 4.40
4605 6882 9.772973 ATCCATATTAATTGTCGCTGTACTAAA 57.227 29.630 0.00 0.00 0.00 1.85
4676 6980 4.816786 TGTTGTGTCACTGAATGATGTG 57.183 40.909 4.27 0.00 40.28 3.21
4703 7007 5.762179 TCTCTTCCAATTCTAAAGAGGCA 57.238 39.130 15.73 1.98 43.94 4.75
5240 7653 7.823745 TTTTTAGCCATCTCTTTTCTGAACT 57.176 32.000 0.00 0.00 0.00 3.01
5381 7801 1.592669 CTGGCAATCCTACGCTCCG 60.593 63.158 0.00 0.00 0.00 4.63
5493 7920 5.493809 TCCTAGGTAACAAACATGCCTAAC 58.506 41.667 9.08 0.00 35.17 2.34
5508 7935 8.112822 TCCAAAAATCATGTCAATTCCTAGGTA 58.887 33.333 9.08 0.00 0.00 3.08
5586 8013 4.912586 TCCGGATGGTAATCAACTTTTCA 58.087 39.130 0.00 0.00 34.17 2.69
5661 8088 1.376543 AGAACGCATGCAGAAGGATG 58.623 50.000 19.57 0.50 45.39 3.51
5726 8154 4.261489 GCTGATAGCCAAGTCCATTCATTG 60.261 45.833 0.00 0.00 34.48 2.82
5783 8211 3.142174 GACAAGTGGGAGGTGAAAAGAG 58.858 50.000 0.00 0.00 0.00 2.85
5926 8358 0.980754 TCGCCCACCACCATGAGTAT 60.981 55.000 0.00 0.00 0.00 2.12
6038 8470 7.927629 CCGAAAATTCCCATTTGACATATTCAT 59.072 33.333 0.00 0.00 32.57 2.57
6048 8480 6.815089 TCCATAATCCGAAAATTCCCATTTG 58.185 36.000 0.00 0.00 32.57 2.32
6141 8573 7.669304 TGTCAATTTTGAGATGGGACTAATTCA 59.331 33.333 0.00 0.00 37.98 2.57
6298 8736 7.155655 TGCATAGCATTTTACATCAACAGAA 57.844 32.000 0.00 0.00 31.71 3.02


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

AutoCloner maintained by Alex Coulton.