Multiple sequence alignment - TraesCS7D01G019900

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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 TraesCS7D01G019900 chr7D 100.000 3095 0 0 1 3095 8562421 8559327 0.000000e+00 5716.0
1 TraesCS7D01G019900 chr7D 100.000 309 0 0 3364 3672 8559058 8558750 4.110000e-159 571.0
2 TraesCS7D01G019900 chr7D 91.515 165 12 1 2929 3091 480042917 480042753 3.690000e-55 226.0
3 TraesCS7D01G019900 chr7D 95.745 47 2 0 2828 2874 413234017 413234063 3.930000e-10 76.8
4 TraesCS7D01G019900 chr4A 95.345 2191 93 5 599 2781 731303943 731306132 0.000000e+00 3472.0
5 TraesCS7D01G019900 chr4A 86.660 997 121 10 924 1912 602250801 602249809 0.000000e+00 1094.0
6 TraesCS7D01G019900 chr4A 88.243 791 67 16 2062 2840 602249715 602248939 0.000000e+00 922.0
7 TraesCS7D01G019900 chr4A 93.522 247 16 0 35 281 731302551 731302797 5.790000e-98 368.0
8 TraesCS7D01G019900 chr4A 86.408 309 42 0 3364 3672 574720628 574720320 4.540000e-89 339.0
9 TraesCS7D01G019900 chr4A 91.589 107 5 1 456 562 731303603 731303705 1.060000e-30 145.0
10 TraesCS7D01G019900 chr7A 91.057 1353 117 2 599 1948 9110719 9109368 0.000000e+00 1825.0
11 TraesCS7D01G019900 chr7A 92.865 939 60 6 1952 2888 9109331 9108398 0.000000e+00 1356.0
12 TraesCS7D01G019900 chr7A 95.588 340 9 2 3 342 9111394 9111061 1.160000e-149 540.0
13 TraesCS7D01G019900 chr7A 94.565 92 4 1 478 569 9111044 9110954 1.370000e-29 141.0
14 TraesCS7D01G019900 chr7A 97.727 44 1 0 2829 2872 678144138 678144181 3.930000e-10 76.8
15 TraesCS7D01G019900 chr7A 92.000 50 2 2 2879 2926 83529718 83529669 6.580000e-08 69.4
16 TraesCS7D01G019900 chr4B 86.354 982 123 7 939 1911 3859533 3860512 0.000000e+00 1061.0
17 TraesCS7D01G019900 chr4B 89.986 709 59 8 2059 2761 3860606 3861308 0.000000e+00 905.0
18 TraesCS7D01G019900 chr4B 92.414 145 6 4 340 479 371434325 371434469 6.220000e-48 202.0
19 TraesCS7D01G019900 chr4B 88.372 86 10 0 478 563 3858850 3858935 1.800000e-18 104.0
20 TraesCS7D01G019900 chr4B 94.118 51 3 0 1952 2002 27399484 27399534 1.090000e-10 78.7
21 TraesCS7D01G019900 chr4B 92.157 51 1 3 2884 2932 544445315 544445266 6.580000e-08 69.4
22 TraesCS7D01G019900 chr4D 89.931 725 63 6 2059 2778 3277676 3278395 0.000000e+00 926.0
23 TraesCS7D01G019900 chr4D 85.439 467 55 7 1457 1916 3277128 3277588 1.190000e-129 473.0
24 TraesCS7D01G019900 chr4D 96.774 124 4 0 341 464 52629730 52629853 1.340000e-49 207.0
25 TraesCS7D01G019900 chr2D 88.997 309 34 0 3364 3672 486963213 486963521 2.070000e-102 383.0
26 TraesCS7D01G019900 chr2D 92.169 166 11 1 2929 3092 486962996 486963161 2.200000e-57 233.0
27 TraesCS7D01G019900 chr2D 97.500 120 3 0 341 460 635794513 635794394 4.810000e-49 206.0
28 TraesCS7D01G019900 chr2D 93.878 49 2 1 2829 2876 422752179 422752131 5.090000e-09 73.1
29 TraesCS7D01G019900 chr2D 81.707 82 11 3 1928 2005 627959739 627959658 8.510000e-07 65.8
30 TraesCS7D01G019900 chr5D 86.731 309 41 0 3364 3672 560557714 560557406 9.760000e-91 344.0
31 TraesCS7D01G019900 chr5D 92.121 165 11 2 2929 3091 451066577 451066741 7.930000e-57 231.0
32 TraesCS7D01G019900 chr5D 98.305 118 2 0 340 457 30459071 30459188 1.340000e-49 207.0
33 TraesCS7D01G019900 chr5D 94.574 129 7 0 340 468 445698091 445698219 2.240000e-47 200.0
34 TraesCS7D01G019900 chr5D 92.727 55 3 1 1952 2006 77075639 77075586 1.090000e-10 78.7
35 TraesCS7D01G019900 chr3B 86.731 309 41 0 3364 3672 368120121 368119813 9.760000e-91 344.0
36 TraesCS7D01G019900 chr3B 98.319 119 2 0 341 459 52921925 52922043 3.720000e-50 209.0
37 TraesCS7D01G019900 chr3B 97.778 45 1 0 2830 2874 669445419 669445463 1.090000e-10 78.7
38 TraesCS7D01G019900 chr3B 90.566 53 2 3 2879 2929 450376600 450376651 2.370000e-07 67.6
39 TraesCS7D01G019900 chr3A 86.688 308 41 0 3365 3672 633730717 633731024 3.510000e-90 342.0
40 TraesCS7D01G019900 chr3A 90.909 165 13 2 2929 3091 281305396 281305232 1.720000e-53 220.0
41 TraesCS7D01G019900 chr3A 90.566 159 12 3 2935 3091 281318833 281318676 1.340000e-49 207.0
42 TraesCS7D01G019900 chr3A 95.918 49 2 0 2828 2876 679696646 679696598 3.040000e-11 80.5
43 TraesCS7D01G019900 chr3A 95.833 48 2 0 2823 2870 436468941 436468988 1.090000e-10 78.7
44 TraesCS7D01G019900 chr3D 86.645 307 41 0 3364 3670 4905988 4905682 1.260000e-89 340.0
45 TraesCS7D01G019900 chr3D 86.408 309 42 0 3364 3672 113577477 113577169 4.540000e-89 339.0
46 TraesCS7D01G019900 chr3D 92.121 165 11 2 2929 3091 234551122 234551286 7.930000e-57 231.0
47 TraesCS7D01G019900 chr3D 97.581 124 3 0 334 457 7308050 7308173 2.870000e-51 213.0
48 TraesCS7D01G019900 chr3D 96.639 119 4 0 339 457 238618560 238618442 8.040000e-47 198.0
49 TraesCS7D01G019900 chr3D 87.273 55 5 2 1952 2006 515824907 515824959 1.100000e-05 62.1
50 TraesCS7D01G019900 chr6B 86.319 307 42 0 3364 3670 548534280 548533974 5.880000e-88 335.0
51 TraesCS7D01G019900 chr6B 90.566 53 1 4 2881 2930 13827570 13827621 2.370000e-07 67.6
52 TraesCS7D01G019900 chr6B 90.385 52 3 2 2879 2928 646750101 646750152 2.370000e-07 67.6
53 TraesCS7D01G019900 chr6B 90.385 52 3 2 2879 2928 646750211 646750262 2.370000e-07 67.6
54 TraesCS7D01G019900 chr6B 90.196 51 4 1 1952 2002 520447582 520447631 8.510000e-07 65.8
55 TraesCS7D01G019900 chr6B 89.091 55 2 3 2884 2935 658611744 658611691 8.510000e-07 65.8
56 TraesCS7D01G019900 chr1A 86.084 309 43 0 3364 3672 369492076 369491768 2.110000e-87 333.0
57 TraesCS7D01G019900 chr1A 100.000 29 0 0 1921 1949 9214110 9214138 2.000000e-03 54.7
58 TraesCS7D01G019900 chr2A 92.025 163 13 0 2929 3091 136927873 136927711 2.850000e-56 230.0
59 TraesCS7D01G019900 chr2A 91.515 165 12 2 2929 3091 136858026 136857862 3.690000e-55 226.0
60 TraesCS7D01G019900 chr2A 100.000 44 0 0 2829 2872 707069333 707069376 8.450000e-12 82.4
61 TraesCS7D01G019900 chr1B 89.759 166 15 1 2928 3091 450603999 450603834 1.030000e-50 211.0
62 TraesCS7D01G019900 chr2B 94.030 134 5 3 326 457 497854289 497854157 2.240000e-47 200.0
63 TraesCS7D01G019900 chr2B 94.118 51 3 0 1952 2002 744815558 744815508 1.090000e-10 78.7
64 TraesCS7D01G019900 chr2B 92.157 51 4 0 1952 2002 659648764 659648814 5.090000e-09 73.1
65 TraesCS7D01G019900 chr5B 96.364 55 2 0 1952 2006 641041044 641041098 1.400000e-14 91.6
66 TraesCS7D01G019900 chr5B 89.286 56 1 5 2879 2932 662596867 662596815 8.510000e-07 65.8
67 TraesCS7D01G019900 chr5B 86.667 60 4 4 2882 2937 664376065 664376124 3.060000e-06 63.9
68 TraesCS7D01G019900 chr5B 88.235 51 6 0 1957 2007 298706526 298706476 1.100000e-05 62.1
69 TraesCS7D01G019900 chr5B 87.273 55 6 1 1952 2006 583196950 583197003 1.100000e-05 62.1
70 TraesCS7D01G019900 chr6D 97.778 45 1 0 2828 2872 292073370 292073414 1.090000e-10 78.7
71 TraesCS7D01G019900 chr6D 90.196 51 2 2 1959 2007 464533667 464533618 3.060000e-06 63.9
72 TraesCS7D01G019900 chr1D 92.157 51 3 1 1952 2002 367383336 367383287 1.830000e-08 71.3


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 TraesCS7D01G019900 chr7D 8558750 8562421 3671 True 3143.500000 5716 100.000000 1 3672 2 chr7D.!!$R2 3671
1 TraesCS7D01G019900 chr4A 731302551 731306132 3581 False 1328.333333 3472 93.485333 35 2781 3 chr4A.!!$F1 2746
2 TraesCS7D01G019900 chr4A 602248939 602250801 1862 True 1008.000000 1094 87.451500 924 2840 2 chr4A.!!$R2 1916
3 TraesCS7D01G019900 chr7A 9108398 9111394 2996 True 965.500000 1825 93.518750 3 2888 4 chr7A.!!$R2 2885
4 TraesCS7D01G019900 chr4B 3858850 3861308 2458 False 690.000000 1061 88.237333 478 2761 3 chr4B.!!$F3 2283
5 TraesCS7D01G019900 chr4D 3277128 3278395 1267 False 699.500000 926 87.685000 1457 2778 2 chr4D.!!$F2 1321
6 TraesCS7D01G019900 chr2D 486962996 486963521 525 False 308.000000 383 90.583000 2929 3672 2 chr2D.!!$F1 743

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
451 1198 0.030369 CGAGTATTTCCGGACGGAGG 59.970 60.0 13.64 0.00 46.06 4.30 F
453 1200 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
910 1934 0.104120 TGGTACAATCAGCCCGATCG 59.896 55.0 8.51 8.51 31.11 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 3041 0.643820 GTCCGGAATTACTTGTCGCG 59.356 55.0 5.23 0.0 0.00 5.87 R
2116 3185 0.907486 TCAGTAGCAGCTCAGCCATT 59.093 50.0 0.00 0.0 34.23 3.16 R
2703 3777 0.664761 GATGATGTTCCCATGCCACG 59.335 55.0 0.00 0.0 0.00 4.94 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
46 47 8.362464 AGAGATATGAAATATAAGCGGTGGTA 57.638 34.615 0.00 0.00 40.26 3.25
117 119 2.523015 CATTTGATTCTGACAAGGCGC 58.477 47.619 0.00 0.00 0.00 6.53
184 186 3.891049 ACAGAAAAAGAGCAGTCCACTT 58.109 40.909 0.00 0.00 0.00 3.16
201 203 7.007723 AGTCCACTTGCTAATAGCTAGACTAT 58.992 38.462 25.72 4.99 44.89 2.12
203 205 8.455682 GTCCACTTGCTAATAGCTAGACTATAG 58.544 40.741 25.72 10.32 44.89 1.31
288 1035 3.250521 GGCTAGTCATAGTGGAGTACGAC 59.749 52.174 0.00 0.00 0.00 4.34
335 1082 4.082300 TGCGGAACATGTTTTGAATGCTAT 60.082 37.500 13.36 0.00 0.00 2.97
336 1083 5.124617 TGCGGAACATGTTTTGAATGCTATA 59.875 36.000 13.36 0.00 0.00 1.31
338 1085 6.020678 GCGGAACATGTTTTGAATGCTATAAC 60.021 38.462 13.36 0.00 0.00 1.89
339 1086 7.026562 CGGAACATGTTTTGAATGCTATAACA 58.973 34.615 13.36 0.00 33.73 2.41
340 1087 7.701924 CGGAACATGTTTTGAATGCTATAACAT 59.298 33.333 13.36 0.00 39.33 2.71
345 1092 9.669353 CATGTTTTGAATGCTATAACATACTCC 57.331 33.333 0.00 0.00 37.34 3.85
346 1093 8.220755 TGTTTTGAATGCTATAACATACTCCC 57.779 34.615 0.00 0.00 0.00 4.30
347 1094 8.052748 TGTTTTGAATGCTATAACATACTCCCT 58.947 33.333 0.00 0.00 0.00 4.20
348 1095 8.560374 GTTTTGAATGCTATAACATACTCCCTC 58.440 37.037 0.00 0.00 0.00 4.30
349 1096 6.360370 TGAATGCTATAACATACTCCCTCC 57.640 41.667 0.00 0.00 0.00 4.30
350 1097 5.047306 TGAATGCTATAACATACTCCCTCCG 60.047 44.000 0.00 0.00 0.00 4.63
351 1098 3.840991 TGCTATAACATACTCCCTCCGT 58.159 45.455 0.00 0.00 0.00 4.69
352 1099 3.825014 TGCTATAACATACTCCCTCCGTC 59.175 47.826 0.00 0.00 0.00 4.79
353 1100 3.193056 GCTATAACATACTCCCTCCGTCC 59.807 52.174 0.00 0.00 0.00 4.79
354 1101 1.683943 TAACATACTCCCTCCGTCCG 58.316 55.000 0.00 0.00 0.00 4.79
355 1102 1.041447 AACATACTCCCTCCGTCCGG 61.041 60.000 0.00 0.00 0.00 5.14
356 1103 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
357 1104 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
358 1105 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
359 1106 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
360 1107 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
361 1108 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
362 1109 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
363 1110 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
364 1111 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
365 1112 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
366 1113 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
367 1114 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
368 1115 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
369 1116 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
370 1117 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
371 1118 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
372 1119 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
373 1120 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
374 1121 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
375 1122 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
376 1123 4.494199 CGGAAATACTTGTCGGAGAAATGC 60.494 45.833 0.00 0.00 39.69 3.56
377 1124 4.394920 GGAAATACTTGTCGGAGAAATGCA 59.605 41.667 0.00 0.00 39.69 3.96
378 1125 5.066505 GGAAATACTTGTCGGAGAAATGCAT 59.933 40.000 0.00 0.00 39.69 3.96
379 1126 6.260050 GGAAATACTTGTCGGAGAAATGCATA 59.740 38.462 0.00 0.00 39.69 3.14
380 1127 7.201696 GGAAATACTTGTCGGAGAAATGCATAA 60.202 37.037 0.00 0.00 39.69 1.90
381 1128 7.624360 AATACTTGTCGGAGAAATGCATAAA 57.376 32.000 0.00 0.00 39.69 1.40
382 1129 5.957842 ACTTGTCGGAGAAATGCATAAAA 57.042 34.783 0.00 0.00 39.69 1.52
383 1130 6.325919 ACTTGTCGGAGAAATGCATAAAAA 57.674 33.333 0.00 0.00 39.69 1.94
384 1131 6.924111 ACTTGTCGGAGAAATGCATAAAAAT 58.076 32.000 0.00 0.00 39.69 1.82
385 1132 6.808212 ACTTGTCGGAGAAATGCATAAAAATG 59.192 34.615 0.00 0.00 39.69 2.32
386 1133 6.507958 TGTCGGAGAAATGCATAAAAATGA 57.492 33.333 0.00 0.00 39.69 2.57
387 1134 6.918626 TGTCGGAGAAATGCATAAAAATGAA 58.081 32.000 0.00 0.00 39.69 2.57
388 1135 7.546358 TGTCGGAGAAATGCATAAAAATGAAT 58.454 30.769 0.00 0.00 39.69 2.57
389 1136 8.681806 TGTCGGAGAAATGCATAAAAATGAATA 58.318 29.630 0.00 0.00 39.69 1.75
390 1137 9.683069 GTCGGAGAAATGCATAAAAATGAATAT 57.317 29.630 0.00 0.00 39.69 1.28
430 1177 6.929625 ACATCTAGATACATCCATTCCTTCG 58.070 40.000 4.54 0.00 0.00 3.79
431 1178 6.721668 ACATCTAGATACATCCATTCCTTCGA 59.278 38.462 4.54 0.00 0.00 3.71
432 1179 6.576662 TCTAGATACATCCATTCCTTCGAC 57.423 41.667 0.00 0.00 0.00 4.20
433 1180 4.244425 AGATACATCCATTCCTTCGACG 57.756 45.455 0.00 0.00 0.00 5.12
434 1181 3.889538 AGATACATCCATTCCTTCGACGA 59.110 43.478 0.00 0.00 0.00 4.20
435 1182 2.586258 ACATCCATTCCTTCGACGAG 57.414 50.000 0.00 0.00 0.00 4.18
436 1183 1.825474 ACATCCATTCCTTCGACGAGT 59.175 47.619 0.00 0.00 0.00 4.18
437 1184 3.021695 ACATCCATTCCTTCGACGAGTA 58.978 45.455 0.00 0.00 0.00 2.59
438 1185 3.637229 ACATCCATTCCTTCGACGAGTAT 59.363 43.478 0.00 0.00 0.00 2.12
439 1186 4.099573 ACATCCATTCCTTCGACGAGTATT 59.900 41.667 0.00 0.00 0.00 1.89
440 1187 4.730949 TCCATTCCTTCGACGAGTATTT 57.269 40.909 0.00 0.00 0.00 1.40
441 1188 4.679662 TCCATTCCTTCGACGAGTATTTC 58.320 43.478 0.00 0.00 0.00 2.17
442 1189 3.802685 CCATTCCTTCGACGAGTATTTCC 59.197 47.826 0.00 0.00 0.00 3.13
443 1190 2.838386 TCCTTCGACGAGTATTTCCG 57.162 50.000 0.00 0.00 0.00 4.30
444 1191 1.402968 TCCTTCGACGAGTATTTCCGG 59.597 52.381 0.00 0.00 0.00 5.14
445 1192 1.402968 CCTTCGACGAGTATTTCCGGA 59.597 52.381 0.00 0.00 0.00 5.14
446 1193 2.448219 CTTCGACGAGTATTTCCGGAC 58.552 52.381 1.83 0.00 0.00 4.79
447 1194 0.374758 TCGACGAGTATTTCCGGACG 59.625 55.000 1.83 5.89 0.00 4.79
448 1195 0.590732 CGACGAGTATTTCCGGACGG 60.591 60.000 1.83 3.96 0.00 4.79
449 1196 0.734889 GACGAGTATTTCCGGACGGA 59.265 55.000 1.83 9.76 43.52 4.69
450 1197 0.737219 ACGAGTATTTCCGGACGGAG 59.263 55.000 13.64 3.15 46.06 4.63
451 1198 0.030369 CGAGTATTTCCGGACGGAGG 59.970 60.000 13.64 0.00 46.06 4.30
452 1199 0.388294 GAGTATTTCCGGACGGAGGG 59.612 60.000 13.64 0.00 46.06 4.30
453 1200 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
454 1201 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
459 1206 1.379576 CCGGACGGAGGGAGTAGTT 60.380 63.158 4.40 0.00 37.50 2.24
469 1216 1.196012 GGGAGTAGTTGACAGAGGGG 58.804 60.000 0.00 0.00 0.00 4.79
476 1223 5.789535 AGTAGTTGACAGAGGGGGTATAAT 58.210 41.667 0.00 0.00 0.00 1.28
477 1224 6.210522 AGTAGTTGACAGAGGGGGTATAATT 58.789 40.000 0.00 0.00 0.00 1.40
478 1225 7.367828 AGTAGTTGACAGAGGGGGTATAATTA 58.632 38.462 0.00 0.00 0.00 1.40
479 1226 7.847848 AGTAGTTGACAGAGGGGGTATAATTAA 59.152 37.037 0.00 0.00 0.00 1.40
538 1285 5.163693 GGCATCATCATCGAATCATGCATAA 60.164 40.000 8.02 0.00 38.71 1.90
545 1292 7.457024 TCATCGAATCATGCATAAATGGATT 57.543 32.000 0.00 3.71 36.67 3.01
587 1337 6.689178 AACATTTTTAAATACTGTGCGCTG 57.311 33.333 9.73 2.21 0.00 5.18
591 1341 7.273381 ACATTTTTAAATACTGTGCGCTGATTC 59.727 33.333 9.73 0.00 0.00 2.52
592 1342 5.871465 TTTAAATACTGTGCGCTGATTCA 57.129 34.783 9.73 0.00 0.00 2.57
594 1344 4.764679 AAATACTGTGCGCTGATTCAAA 57.235 36.364 9.73 0.00 0.00 2.69
722 1723 7.574030 TGCCATGCATGATTTCAAAAAGAAATG 60.574 33.333 28.31 5.81 44.10 2.32
763 1784 2.202440 AACGGTCGTCTCGATGCG 60.202 61.111 0.00 2.85 38.42 4.73
767 1788 1.532343 CGGTCGTCTCGATGCGATTG 61.532 60.000 13.20 6.73 38.42 2.67
789 1810 5.676552 TGGTGCTAGAAGAAAGTACACAAA 58.323 37.500 0.00 0.00 31.90 2.83
793 1814 5.236478 TGCTAGAAGAAAGTACACAAAGCAC 59.764 40.000 0.00 0.00 31.78 4.40
818 1842 1.833787 TTCCTACCCCCGACAGCAAC 61.834 60.000 0.00 0.00 0.00 4.17
910 1934 0.104120 TGGTACAATCAGCCCGATCG 59.896 55.000 8.51 8.51 31.11 3.69
1072 2099 3.012047 TGTGTACCTCCTAGGCCTCTTAA 59.988 47.826 9.68 0.00 39.63 1.85
1081 2108 0.693049 AGGCCTCTTAACCCACAGTG 59.307 55.000 0.00 0.00 0.00 3.66
1086 2113 0.682852 TCTTAACCCACAGTGGTCGG 59.317 55.000 18.82 5.82 37.76 4.79
1092 2119 1.189524 CCCACAGTGGTCGGAACCTA 61.190 60.000 18.82 0.00 46.60 3.08
1245 2272 2.493973 GTCGCCTCCTCAGCAGAG 59.506 66.667 0.00 0.00 41.72 3.35
1545 2572 3.504863 CTTTACGACAGCGCTTAACCTA 58.495 45.455 7.50 0.00 42.48 3.08
1604 2631 2.434884 CGACCGCCATGTCAAGCT 60.435 61.111 0.00 0.00 34.88 3.74
1731 2758 1.549170 AGACGTATCGAGGGCTTGTTT 59.451 47.619 0.00 0.00 0.00 2.83
1780 2807 0.807275 CATCGAGCTTCACATGCGGA 60.807 55.000 0.00 0.00 35.28 5.54
1972 3041 6.756074 TCGCACATCCATTTTTATTCATTTCC 59.244 34.615 0.00 0.00 0.00 3.13
1992 3061 1.717194 GCGACAAGTAATTCCGGACA 58.283 50.000 1.83 0.00 0.00 4.02
2020 3089 4.298626 AGTAGTATTCCTCCATGCTTCCA 58.701 43.478 0.00 0.00 0.00 3.53
2028 3097 1.554160 CTCCATGCTTCCACTCTCTGT 59.446 52.381 0.00 0.00 0.00 3.41
2104 3173 0.108329 CGGATACAAGTTCGGCCACT 60.108 55.000 2.24 0.00 0.00 4.00
2116 3185 2.283101 GCCACTGTGGAATGGGCA 60.283 61.111 30.23 0.00 40.96 5.36
2122 3191 0.974010 CTGTGGAATGGGCAATGGCT 60.974 55.000 6.78 0.00 40.87 4.75
2182 3251 2.094494 TCAAGAGCTCGACCAAGTGATC 60.094 50.000 8.37 0.00 0.00 2.92
2685 3754 5.684184 CGCCAGTTTGAATGTAATCATCATG 59.316 40.000 0.00 0.00 32.56 3.07
2703 3777 2.543777 TGTACTTTGCACCTGACCTC 57.456 50.000 0.00 0.00 0.00 3.85
2785 3869 8.475331 TGCTTTATACTGCTACTAGTGAAAAC 57.525 34.615 5.39 0.00 32.19 2.43
2803 3887 7.724061 AGTGAAAACAGGTTGTATGGTCTATTT 59.276 33.333 0.00 0.00 0.00 1.40
2804 3888 8.021396 GTGAAAACAGGTTGTATGGTCTATTTC 58.979 37.037 0.00 0.00 0.00 2.17
2805 3889 7.721842 TGAAAACAGGTTGTATGGTCTATTTCA 59.278 33.333 0.00 0.00 31.66 2.69
2826 3910 3.064207 AGTACATGTGCTTGTGTTACCG 58.936 45.455 11.03 0.00 0.00 4.02
2841 3926 1.135094 TACCGACTACTCCCTCCGAT 58.865 55.000 0.00 0.00 0.00 4.18
2842 3927 0.179023 ACCGACTACTCCCTCCGATC 60.179 60.000 0.00 0.00 0.00 3.69
2843 3928 0.890090 CCGACTACTCCCTCCGATCC 60.890 65.000 0.00 0.00 0.00 3.36
2844 3929 0.179026 CGACTACTCCCTCCGATCCA 60.179 60.000 0.00 0.00 0.00 3.41
2845 3930 1.545875 CGACTACTCCCTCCGATCCAT 60.546 57.143 0.00 0.00 0.00 3.41
2855 3940 4.905456 TCCCTCCGATCCATAATAAGTGTT 59.095 41.667 0.00 0.00 0.00 3.32
2856 3941 4.997395 CCCTCCGATCCATAATAAGTGTTG 59.003 45.833 0.00 0.00 0.00 3.33
2874 3959 7.826260 AGTGTTGTGGTTTTAGTTCAAAATG 57.174 32.000 0.00 0.00 38.36 2.32
2884 3969 8.290325 GGTTTTAGTTCAAAATGAGGAGTACTG 58.710 37.037 0.00 0.00 38.36 2.74
2885 3970 9.052759 GTTTTAGTTCAAAATGAGGAGTACTGA 57.947 33.333 0.00 0.00 38.36 3.41
2886 3971 9.793259 TTTTAGTTCAAAATGAGGAGTACTGAT 57.207 29.630 0.00 0.00 31.05 2.90
2887 3972 9.436957 TTTAGTTCAAAATGAGGAGTACTGATC 57.563 33.333 0.00 0.00 0.00 2.92
2888 3973 7.251321 AGTTCAAAATGAGGAGTACTGATCT 57.749 36.000 0.00 0.00 0.00 2.75
2889 3974 8.367660 AGTTCAAAATGAGGAGTACTGATCTA 57.632 34.615 0.00 0.00 0.00 1.98
2890 3975 8.816894 AGTTCAAAATGAGGAGTACTGATCTAA 58.183 33.333 0.00 0.00 0.00 2.10
2891 3976 9.436957 GTTCAAAATGAGGAGTACTGATCTAAA 57.563 33.333 0.00 0.00 0.00 1.85
2892 3977 9.436957 TTCAAAATGAGGAGTACTGATCTAAAC 57.563 33.333 0.00 0.00 0.00 2.01
2893 3978 8.593679 TCAAAATGAGGAGTACTGATCTAAACA 58.406 33.333 0.00 0.00 0.00 2.83
2894 3979 8.660373 CAAAATGAGGAGTACTGATCTAAACAC 58.340 37.037 0.00 0.00 0.00 3.32
2895 3980 7.726033 AATGAGGAGTACTGATCTAAACACT 57.274 36.000 0.00 0.00 0.00 3.55
2896 3981 6.761099 TGAGGAGTACTGATCTAAACACTC 57.239 41.667 0.00 0.19 33.31 3.51
2897 3982 6.486056 TGAGGAGTACTGATCTAAACACTCT 58.514 40.000 0.00 0.00 34.28 3.24
2898 3983 6.948886 TGAGGAGTACTGATCTAAACACTCTT 59.051 38.462 0.00 0.00 34.28 2.85
2899 3984 8.107729 TGAGGAGTACTGATCTAAACACTCTTA 58.892 37.037 0.00 0.00 34.28 2.10
2900 3985 9.127277 GAGGAGTACTGATCTAAACACTCTTAT 57.873 37.037 0.00 0.00 34.28 1.73
2914 3999 8.502105 AAACACTCTTATATTTCTTTACGGGG 57.498 34.615 0.00 0.00 0.00 5.73
2915 4000 7.427989 ACACTCTTATATTTCTTTACGGGGA 57.572 36.000 0.00 0.00 0.00 4.81
2916 4001 7.498443 ACACTCTTATATTTCTTTACGGGGAG 58.502 38.462 0.00 0.00 0.00 4.30
2917 4002 7.125356 ACACTCTTATATTTCTTTACGGGGAGT 59.875 37.037 0.00 0.00 0.00 3.85
2918 4003 8.636213 CACTCTTATATTTCTTTACGGGGAGTA 58.364 37.037 0.00 0.00 0.00 2.59
2919 4004 8.637099 ACTCTTATATTTCTTTACGGGGAGTAC 58.363 37.037 0.00 0.00 34.56 2.73
2920 4005 8.537728 TCTTATATTTCTTTACGGGGAGTACA 57.462 34.615 0.00 0.00 34.56 2.90
2921 4006 9.151177 TCTTATATTTCTTTACGGGGAGTACAT 57.849 33.333 0.00 0.00 34.56 2.29
2924 4009 6.803366 ATTTCTTTACGGGGAGTACATACT 57.197 37.500 0.00 0.00 39.71 2.12
2925 4010 6.610075 TTTCTTTACGGGGAGTACATACTT 57.390 37.500 0.00 0.00 36.50 2.24
2926 4011 7.716799 TTTCTTTACGGGGAGTACATACTTA 57.283 36.000 0.00 0.00 36.50 2.24
2927 4012 7.902920 TTCTTTACGGGGAGTACATACTTAT 57.097 36.000 0.00 0.00 36.50 1.73
2950 4035 6.509418 TTGTAGAAAGGTATTGGATGCAAC 57.491 37.500 0.12 0.00 0.00 4.17
2961 4046 7.342799 AGGTATTGGATGCAACTCAATTGTATT 59.657 33.333 0.12 0.00 42.98 1.89
2965 4050 6.798482 TGGATGCAACTCAATTGTATTCATC 58.202 36.000 5.13 11.96 42.25 2.92
3019 4106 2.289195 CGTGACAAGCCAACTAACCCTA 60.289 50.000 0.00 0.00 0.00 3.53
3028 4115 4.975794 AGCCAACTAACCCTACCATATCTT 59.024 41.667 0.00 0.00 0.00 2.40
3032 4119 7.450903 CCAACTAACCCTACCATATCTTTAGG 58.549 42.308 0.00 0.00 33.35 2.69
3058 4145 8.719645 AGTCAATCTATACAAGGCTAGAGATT 57.280 34.615 0.00 0.86 35.83 2.40
3388 4475 2.784347 CAAAGACTGGAAGGGAACTCC 58.216 52.381 0.00 0.00 42.68 3.85
3397 4484 2.791253 AGGGAACTCCTGGAATGCA 58.209 52.632 0.00 0.00 46.07 3.96
3408 4495 1.180456 TGGAATGCAGTGGTTGGCAG 61.180 55.000 0.00 0.00 44.24 4.85
3414 4501 3.511610 AGTGGTTGGCAGCCCCTT 61.512 61.111 18.29 0.11 0.00 3.95
3415 4502 3.305516 GTGGTTGGCAGCCCCTTG 61.306 66.667 18.29 0.00 0.00 3.61
3428 4515 1.967319 CCCCTTGGTCATAATGTCGG 58.033 55.000 0.00 0.00 0.00 4.79
3447 4534 0.872388 GCAAACTGTTGGGTAGTCGG 59.128 55.000 0.00 0.00 35.10 4.79
3492 4579 0.319641 AACTGAACCTTCTCGCGGAC 60.320 55.000 6.13 0.00 0.00 4.79
3504 4591 3.491934 CGCGGACGAAATGAACATC 57.508 52.632 0.00 0.00 43.93 3.06
3507 4594 1.005975 GCGGACGAAATGAACATCGAG 60.006 52.381 1.84 0.00 41.43 4.04
3539 4626 2.044888 GGTGTGTTTATGTTGCACCG 57.955 50.000 0.00 0.00 39.90 4.94
3544 4631 3.241701 GTGTTTATGTTGCACCGGATTG 58.758 45.455 9.46 0.00 0.00 2.67
3546 4633 0.814457 TTATGTTGCACCGGATTGGC 59.186 50.000 9.46 6.85 43.94 4.52
3560 4647 0.466189 ATTGGCCGCAAGATAGGTGG 60.466 55.000 0.00 0.00 43.02 4.61
3571 4658 4.196193 CAAGATAGGTGGCCGAAACATTA 58.804 43.478 0.00 0.00 0.00 1.90
3574 4661 2.799126 AGGTGGCCGAAACATTATCA 57.201 45.000 0.00 0.00 0.00 2.15
3575 4662 3.297134 AGGTGGCCGAAACATTATCAT 57.703 42.857 0.00 0.00 0.00 2.45
3577 4664 4.787551 AGGTGGCCGAAACATTATCATAA 58.212 39.130 0.00 0.00 0.00 1.90
3580 4667 5.977129 GGTGGCCGAAACATTATCATAAAAG 59.023 40.000 0.00 0.00 0.00 2.27
3608 4695 0.261991 AGCCTTCGGGATAGAGACCA 59.738 55.000 0.00 0.00 37.25 4.02
3624 4711 4.061596 GAGACCAGAAGTTCACCAAGAAG 58.938 47.826 5.50 0.00 36.78 2.85
3640 4727 1.134220 AGAAGGTGACGCAACCAAGAA 60.134 47.619 9.58 0.00 43.20 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.100344 TGAGCTACCACCGCTTATATTTCA 59.900 41.667 0.00 0.00 37.96 2.69
46 47 1.613925 TCGTCAGCTGTTAGTTGAGCT 59.386 47.619 14.67 0.00 46.73 4.09
92 93 1.851304 TGTCAGAATCAAATGGGGCC 58.149 50.000 0.00 0.00 0.00 5.80
117 119 4.101790 GGTGTTGATGCGCCACCG 62.102 66.667 15.49 0.00 39.29 4.94
184 186 6.722328 TCTGCCTATAGTCTAGCTATTAGCA 58.278 40.000 17.59 18.53 45.56 3.49
201 203 2.967887 TGCTGAAGATATGCTCTGCCTA 59.032 45.455 8.95 0.00 33.29 3.93
203 205 1.872313 GTGCTGAAGATATGCTCTGCC 59.128 52.381 8.95 0.71 33.29 4.85
335 1082 1.683943 CGGACGGAGGGAGTATGTTA 58.316 55.000 0.00 0.00 0.00 2.41
336 1083 1.041447 CCGGACGGAGGGAGTATGTT 61.041 60.000 4.40 0.00 37.50 2.71
338 1085 0.754217 TTCCGGACGGAGGGAGTATG 60.754 60.000 13.64 0.00 46.06 2.39
339 1086 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
340 1087 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
341 1088 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
342 1089 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
343 1090 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
344 1091 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
345 1092 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
346 1093 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
347 1094 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
348 1095 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
349 1096 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
350 1097 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
351 1098 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
352 1099 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
353 1100 4.494199 GCATTTCTCCGACAAGTATTTCCG 60.494 45.833 0.00 0.00 0.00 4.30
354 1101 4.394920 TGCATTTCTCCGACAAGTATTTCC 59.605 41.667 0.00 0.00 0.00 3.13
355 1102 5.545658 TGCATTTCTCCGACAAGTATTTC 57.454 39.130 0.00 0.00 0.00 2.17
356 1103 7.624360 TTATGCATTTCTCCGACAAGTATTT 57.376 32.000 3.54 0.00 0.00 1.40
357 1104 7.624360 TTTATGCATTTCTCCGACAAGTATT 57.376 32.000 3.54 0.00 0.00 1.89
358 1105 7.624360 TTTTATGCATTTCTCCGACAAGTAT 57.376 32.000 3.54 0.00 0.00 2.12
359 1106 7.441890 TTTTTATGCATTTCTCCGACAAGTA 57.558 32.000 3.54 0.00 0.00 2.24
360 1107 5.957842 TTTTATGCATTTCTCCGACAAGT 57.042 34.783 3.54 0.00 0.00 3.16
361 1108 7.028962 TCATTTTTATGCATTTCTCCGACAAG 58.971 34.615 3.54 0.00 0.00 3.16
362 1109 6.918626 TCATTTTTATGCATTTCTCCGACAA 58.081 32.000 3.54 0.00 0.00 3.18
363 1110 6.507958 TCATTTTTATGCATTTCTCCGACA 57.492 33.333 3.54 0.00 0.00 4.35
364 1111 7.992180 ATTCATTTTTATGCATTTCTCCGAC 57.008 32.000 3.54 0.00 0.00 4.79
404 1151 8.690884 CGAAGGAATGGATGTATCTAGATGTAT 58.309 37.037 15.79 9.11 0.00 2.29
405 1152 7.888546 TCGAAGGAATGGATGTATCTAGATGTA 59.111 37.037 15.79 4.44 0.00 2.29
406 1153 6.721668 TCGAAGGAATGGATGTATCTAGATGT 59.278 38.462 15.79 1.25 0.00 3.06
407 1154 7.032580 GTCGAAGGAATGGATGTATCTAGATG 58.967 42.308 15.79 0.00 0.00 2.90
408 1155 6.127869 CGTCGAAGGAATGGATGTATCTAGAT 60.128 42.308 10.73 10.73 0.00 1.98
409 1156 5.181433 CGTCGAAGGAATGGATGTATCTAGA 59.819 44.000 0.00 0.00 0.00 2.43
410 1157 5.181433 TCGTCGAAGGAATGGATGTATCTAG 59.819 44.000 0.00 0.00 0.00 2.43
411 1158 5.067954 TCGTCGAAGGAATGGATGTATCTA 58.932 41.667 0.00 0.00 0.00 1.98
412 1159 3.889538 TCGTCGAAGGAATGGATGTATCT 59.110 43.478 0.00 0.00 0.00 1.98
413 1160 4.230657 CTCGTCGAAGGAATGGATGTATC 58.769 47.826 0.00 0.00 0.00 2.24
414 1161 3.637229 ACTCGTCGAAGGAATGGATGTAT 59.363 43.478 0.00 0.00 0.00 2.29
415 1162 3.021695 ACTCGTCGAAGGAATGGATGTA 58.978 45.455 0.00 0.00 0.00 2.29
416 1163 1.825474 ACTCGTCGAAGGAATGGATGT 59.175 47.619 0.00 0.00 0.00 3.06
417 1164 2.586258 ACTCGTCGAAGGAATGGATG 57.414 50.000 0.00 0.00 0.00 3.51
418 1165 4.939052 AATACTCGTCGAAGGAATGGAT 57.061 40.909 0.00 0.00 0.00 3.41
419 1166 4.441079 GGAAATACTCGTCGAAGGAATGGA 60.441 45.833 0.00 0.00 0.00 3.41
420 1167 3.802685 GGAAATACTCGTCGAAGGAATGG 59.197 47.826 0.00 0.00 0.00 3.16
421 1168 3.486108 CGGAAATACTCGTCGAAGGAATG 59.514 47.826 0.00 0.00 0.00 2.67
422 1169 3.490419 CCGGAAATACTCGTCGAAGGAAT 60.490 47.826 0.00 0.00 0.00 3.01
423 1170 2.159338 CCGGAAATACTCGTCGAAGGAA 60.159 50.000 0.00 0.00 0.00 3.36
424 1171 1.402968 CCGGAAATACTCGTCGAAGGA 59.597 52.381 0.00 0.00 0.00 3.36
425 1172 1.402968 TCCGGAAATACTCGTCGAAGG 59.597 52.381 0.00 0.00 0.00 3.46
426 1173 2.448219 GTCCGGAAATACTCGTCGAAG 58.552 52.381 5.23 0.00 0.00 3.79
427 1174 1.202065 CGTCCGGAAATACTCGTCGAA 60.202 52.381 5.23 0.00 0.00 3.71
428 1175 0.374758 CGTCCGGAAATACTCGTCGA 59.625 55.000 5.23 0.00 0.00 4.20
429 1176 0.590732 CCGTCCGGAAATACTCGTCG 60.591 60.000 5.23 1.25 37.50 5.12
430 1177 0.734889 TCCGTCCGGAAATACTCGTC 59.265 55.000 5.23 0.00 42.05 4.20
431 1178 0.737219 CTCCGTCCGGAAATACTCGT 59.263 55.000 5.23 0.00 44.66 4.18
432 1179 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.000 5.23 3.90 44.66 4.18
433 1180 0.388294 CCCTCCGTCCGGAAATACTC 59.612 60.000 5.23 0.00 44.66 2.59
434 1181 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
435 1182 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
436 1183 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
437 1184 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
438 1185 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
439 1186 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
440 1187 1.856539 AACTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
441 1188 1.379576 AACTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
442 1189 0.679002 TCAACTACTCCCTCCGTCCG 60.679 60.000 0.00 0.00 0.00 4.79
443 1190 0.816373 GTCAACTACTCCCTCCGTCC 59.184 60.000 0.00 0.00 0.00 4.79
444 1191 1.473278 CTGTCAACTACTCCCTCCGTC 59.527 57.143 0.00 0.00 0.00 4.79
445 1192 1.075050 TCTGTCAACTACTCCCTCCGT 59.925 52.381 0.00 0.00 0.00 4.69
446 1193 1.746220 CTCTGTCAACTACTCCCTCCG 59.254 57.143 0.00 0.00 0.00 4.63
447 1194 2.104170 CCTCTGTCAACTACTCCCTCC 58.896 57.143 0.00 0.00 0.00 4.30
448 1195 2.104170 CCCTCTGTCAACTACTCCCTC 58.896 57.143 0.00 0.00 0.00 4.30
449 1196 1.273324 CCCCTCTGTCAACTACTCCCT 60.273 57.143 0.00 0.00 0.00 4.20
450 1197 1.196012 CCCCTCTGTCAACTACTCCC 58.804 60.000 0.00 0.00 0.00 4.30
451 1198 1.196012 CCCCCTCTGTCAACTACTCC 58.804 60.000 0.00 0.00 0.00 3.85
452 1199 1.939980 ACCCCCTCTGTCAACTACTC 58.060 55.000 0.00 0.00 0.00 2.59
453 1200 3.778622 ATACCCCCTCTGTCAACTACT 57.221 47.619 0.00 0.00 0.00 2.57
454 1201 6.496144 AATTATACCCCCTCTGTCAACTAC 57.504 41.667 0.00 0.00 0.00 2.73
459 1206 5.224441 AGCTTAATTATACCCCCTCTGTCA 58.776 41.667 0.00 0.00 0.00 3.58
476 1223 5.633601 CGTGTCTCATAAACTGTGAGCTTAA 59.366 40.000 0.00 0.00 42.17 1.85
477 1224 5.048294 TCGTGTCTCATAAACTGTGAGCTTA 60.048 40.000 0.00 0.00 42.17 3.09
478 1225 3.990469 CGTGTCTCATAAACTGTGAGCTT 59.010 43.478 0.00 0.00 42.17 3.74
479 1226 3.255888 TCGTGTCTCATAAACTGTGAGCT 59.744 43.478 0.00 0.00 42.17 4.09
563 1313 6.920758 TCAGCGCACAGTATTTAAAAATGTTT 59.079 30.769 11.47 0.00 0.00 2.83
564 1314 6.442952 TCAGCGCACAGTATTTAAAAATGTT 58.557 32.000 11.47 0.00 0.00 2.71
566 1316 7.273164 TGAATCAGCGCACAGTATTTAAAAATG 59.727 33.333 11.47 0.00 0.00 2.32
567 1317 7.312154 TGAATCAGCGCACAGTATTTAAAAAT 58.688 30.769 11.47 0.00 0.00 1.82
569 1319 6.247727 TGAATCAGCGCACAGTATTTAAAA 57.752 33.333 11.47 0.00 0.00 1.52
572 1322 5.871465 TTTGAATCAGCGCACAGTATTTA 57.129 34.783 11.47 0.00 0.00 1.40
573 1323 4.764679 TTTGAATCAGCGCACAGTATTT 57.235 36.364 11.47 0.00 0.00 1.40
574 1324 4.970662 ATTTGAATCAGCGCACAGTATT 57.029 36.364 11.47 0.91 0.00 1.89
575 1325 5.359756 TCTATTTGAATCAGCGCACAGTAT 58.640 37.500 11.47 0.00 0.00 2.12
577 1327 3.599343 TCTATTTGAATCAGCGCACAGT 58.401 40.909 11.47 0.00 0.00 3.55
578 1328 4.604843 TTCTATTTGAATCAGCGCACAG 57.395 40.909 11.47 0.00 0.00 3.66
581 1331 7.552458 TTCTATTTCTATTTGAATCAGCGCA 57.448 32.000 11.47 0.00 34.24 6.09
582 1332 9.455847 AATTTCTATTTCTATTTGAATCAGCGC 57.544 29.630 0.00 0.00 34.24 5.92
591 1341 8.677148 TCCTCCCGAATTTCTATTTCTATTTG 57.323 34.615 0.00 0.00 0.00 2.32
592 1342 7.939588 CCTCCTCCCGAATTTCTATTTCTATTT 59.060 37.037 0.00 0.00 0.00 1.40
594 1344 6.013293 CCCTCCTCCCGAATTTCTATTTCTAT 60.013 42.308 0.00 0.00 0.00 1.98
763 1784 5.932303 TGTGTACTTTCTTCTAGCACCAATC 59.068 40.000 0.00 0.00 0.00 2.67
767 1788 5.334182 GCTTTGTGTACTTTCTTCTAGCACC 60.334 44.000 0.00 0.00 0.00 5.01
789 1810 0.846693 GGGGTAGGAATGATGGTGCT 59.153 55.000 0.00 0.00 0.00 4.40
793 1814 0.396811 GTCGGGGGTAGGAATGATGG 59.603 60.000 0.00 0.00 0.00 3.51
818 1842 2.240493 AGTCACTCAAGGGTGAAACG 57.760 50.000 4.02 0.00 46.00 3.60
910 1934 2.717011 CGTGTAATCGCACCACAAAAAC 59.283 45.455 0.00 0.00 36.08 2.43
1072 2099 2.814835 GGTTCCGACCACTGTGGGT 61.815 63.158 29.05 15.53 45.77 4.51
1081 2108 3.464494 CGGGGGTAGGTTCCGACC 61.464 72.222 11.78 11.78 45.96 4.79
1221 2248 4.131088 GAGGAGGCGACCACGGTC 62.131 72.222 6.12 6.12 41.40 4.79
1503 2530 4.309950 AGGTGGCCGACGTGAACC 62.310 66.667 0.00 0.00 0.00 3.62
1517 2544 1.003718 GCTGTCGTAAAGGCCAGGT 60.004 57.895 5.01 0.00 0.00 4.00
1545 2572 2.625617 GGAGAAGATGGTGGAGGAGAGT 60.626 54.545 0.00 0.00 0.00 3.24
1604 2631 2.434331 CGGCCTTGAACTCCCCAA 59.566 61.111 0.00 0.00 0.00 4.12
1653 2680 4.566488 GGGATGAAGTCTGACAGATTTGGT 60.566 45.833 17.04 6.12 0.00 3.67
1659 2686 3.175438 TCAGGGATGAAGTCTGACAGA 57.825 47.619 10.88 0.00 33.21 3.41
1731 2758 2.361483 ATGGCATGCAACCGCTGA 60.361 55.556 21.36 0.00 39.64 4.26
1800 2833 6.677187 GCACGTCTAGGAAGTTTTTCTTTGTT 60.677 38.462 0.00 0.00 36.40 2.83
1921 2955 6.793505 AGTAATTCAAGACGGAGGAAGTAT 57.206 37.500 0.00 0.00 0.00 2.12
1972 3041 0.643820 GTCCGGAATTACTTGTCGCG 59.356 55.000 5.23 0.00 0.00 5.87
2020 3089 4.380655 GCGTGAGGTAACAATACAGAGAGT 60.381 45.833 0.00 0.00 41.41 3.24
2028 3097 2.753055 TGCAGCGTGAGGTAACAATA 57.247 45.000 0.00 0.00 41.81 1.90
2104 3173 1.078891 AGCCATTGCCCATTCCACA 59.921 52.632 0.00 0.00 38.69 4.17
2116 3185 0.907486 TCAGTAGCAGCTCAGCCATT 59.093 50.000 0.00 0.00 34.23 3.16
2122 3191 2.767960 TGATGGATTCAGTAGCAGCTCA 59.232 45.455 0.00 0.00 0.00 4.26
2290 3359 4.338539 GTCGTCTCCGCCACGTGT 62.339 66.667 15.65 0.00 38.45 4.49
2377 3446 2.895372 GGCCATACCTTGCCGTCG 60.895 66.667 0.00 0.00 38.00 5.12
2395 3464 1.134371 GGCATAAACTTCTCCGGCTCT 60.134 52.381 0.00 0.00 0.00 4.09
2437 3506 2.111999 CTCGGCCCTTGAAGTCCACA 62.112 60.000 0.00 0.00 0.00 4.17
2685 3754 1.270147 ACGAGGTCAGGTGCAAAGTAC 60.270 52.381 0.00 0.00 0.00 2.73
2703 3777 0.664761 GATGATGTTCCCATGCCACG 59.335 55.000 0.00 0.00 0.00 4.94
2785 3869 7.327975 TGTACTGAAATAGACCATACAACCTG 58.672 38.462 0.00 0.00 0.00 4.00
2803 3887 4.062293 GGTAACACAAGCACATGTACTGA 58.938 43.478 0.00 0.00 30.84 3.41
2804 3888 3.120683 CGGTAACACAAGCACATGTACTG 60.121 47.826 0.00 0.00 30.84 2.74
2805 3889 3.064207 CGGTAACACAAGCACATGTACT 58.936 45.455 0.00 0.00 30.84 2.73
2826 3910 2.296073 ATGGATCGGAGGGAGTAGTC 57.704 55.000 0.00 0.00 0.00 2.59
2841 3926 8.927675 ACTAAAACCACAACACTTATTATGGA 57.072 30.769 0.00 0.00 0.00 3.41
2842 3927 9.620660 GAACTAAAACCACAACACTTATTATGG 57.379 33.333 0.00 0.00 0.00 2.74
2855 3940 6.605594 ACTCCTCATTTTGAACTAAAACCACA 59.394 34.615 0.00 0.00 40.80 4.17
2856 3941 7.039313 ACTCCTCATTTTGAACTAAAACCAC 57.961 36.000 0.00 0.00 40.80 4.16
2865 3950 9.436957 TTTAGATCAGTACTCCTCATTTTGAAC 57.563 33.333 0.00 0.00 0.00 3.18
2874 3959 7.399245 AAGAGTGTTTAGATCAGTACTCCTC 57.601 40.000 0.00 0.00 36.18 3.71
2888 3973 9.603921 CCCCGTAAAGAAATATAAGAGTGTTTA 57.396 33.333 0.00 0.00 0.00 2.01
2889 3974 8.323567 TCCCCGTAAAGAAATATAAGAGTGTTT 58.676 33.333 0.00 0.00 0.00 2.83
2890 3975 7.854337 TCCCCGTAAAGAAATATAAGAGTGTT 58.146 34.615 0.00 0.00 0.00 3.32
2891 3976 7.125356 ACTCCCCGTAAAGAAATATAAGAGTGT 59.875 37.037 0.00 0.00 0.00 3.55
2892 3977 7.498443 ACTCCCCGTAAAGAAATATAAGAGTG 58.502 38.462 0.00 0.00 0.00 3.51
2893 3978 7.672122 ACTCCCCGTAAAGAAATATAAGAGT 57.328 36.000 0.00 0.00 0.00 3.24
2894 3979 8.636213 TGTACTCCCCGTAAAGAAATATAAGAG 58.364 37.037 0.00 0.00 0.00 2.85
2895 3980 8.537728 TGTACTCCCCGTAAAGAAATATAAGA 57.462 34.615 0.00 0.00 0.00 2.10
2898 3983 9.592196 AGTATGTACTCCCCGTAAAGAAATATA 57.408 33.333 0.00 0.00 0.00 0.86
2899 3984 8.488308 AGTATGTACTCCCCGTAAAGAAATAT 57.512 34.615 0.00 0.00 0.00 1.28
2900 3985 7.902920 AGTATGTACTCCCCGTAAAGAAATA 57.097 36.000 0.00 0.00 0.00 1.40
2901 3986 6.803366 AGTATGTACTCCCCGTAAAGAAAT 57.197 37.500 0.00 0.00 0.00 2.17
2902 3987 6.610075 AAGTATGTACTCCCCGTAAAGAAA 57.390 37.500 0.00 0.00 34.99 2.52
2903 3988 7.902920 ATAAGTATGTACTCCCCGTAAAGAA 57.097 36.000 0.00 0.00 34.99 2.52
2904 3989 7.342799 ACAATAAGTATGTACTCCCCGTAAAGA 59.657 37.037 0.00 0.00 34.99 2.52
2905 3990 7.495055 ACAATAAGTATGTACTCCCCGTAAAG 58.505 38.462 0.00 0.00 34.99 1.85
2906 3991 7.422465 ACAATAAGTATGTACTCCCCGTAAA 57.578 36.000 0.00 0.00 34.99 2.01
2907 3992 7.998383 TCTACAATAAGTATGTACTCCCCGTAA 59.002 37.037 0.00 0.00 34.99 3.18
2908 3993 7.517320 TCTACAATAAGTATGTACTCCCCGTA 58.483 38.462 0.00 0.00 34.99 4.02
2909 3994 6.367983 TCTACAATAAGTATGTACTCCCCGT 58.632 40.000 0.00 0.00 34.99 5.28
2910 3995 6.889301 TCTACAATAAGTATGTACTCCCCG 57.111 41.667 0.00 0.00 34.99 5.73
2911 3996 8.148999 CCTTTCTACAATAAGTATGTACTCCCC 58.851 40.741 0.00 0.00 34.99 4.81
2912 3997 8.702819 ACCTTTCTACAATAAGTATGTACTCCC 58.297 37.037 0.00 0.00 34.99 4.30
2921 4006 9.555727 GCATCCAATACCTTTCTACAATAAGTA 57.444 33.333 0.00 0.00 0.00 2.24
2922 4007 8.052748 TGCATCCAATACCTTTCTACAATAAGT 58.947 33.333 0.00 0.00 0.00 2.24
2923 4008 8.450578 TGCATCCAATACCTTTCTACAATAAG 57.549 34.615 0.00 0.00 0.00 1.73
2924 4009 8.682710 GTTGCATCCAATACCTTTCTACAATAA 58.317 33.333 0.00 0.00 32.75 1.40
2925 4010 8.052748 AGTTGCATCCAATACCTTTCTACAATA 58.947 33.333 0.00 0.00 32.75 1.90
2926 4011 6.891908 AGTTGCATCCAATACCTTTCTACAAT 59.108 34.615 0.00 0.00 32.75 2.71
2927 4012 6.245408 AGTTGCATCCAATACCTTTCTACAA 58.755 36.000 0.00 0.00 32.75 2.41
2950 4035 6.045318 ACAGACTCCGATGAATACAATTGAG 58.955 40.000 13.59 0.00 0.00 3.02
2961 4046 7.576861 TGTATATTGTAACAGACTCCGATGA 57.423 36.000 0.00 0.00 0.00 2.92
2965 4050 7.704271 TCTCTTGTATATTGTAACAGACTCCG 58.296 38.462 0.00 0.00 0.00 4.63
3007 4094 7.291651 TCCTAAAGATATGGTAGGGTTAGTTGG 59.708 40.741 0.00 0.00 35.95 3.77
3028 4115 8.225416 TCTAGCCTTGTATAGATTGACTCCTAA 58.775 37.037 0.00 0.00 0.00 2.69
3032 4119 7.753309 TCTCTAGCCTTGTATAGATTGACTC 57.247 40.000 0.00 0.00 0.00 3.36
3366 4453 0.875059 GTTCCCTTCCAGTCTTTGCG 59.125 55.000 0.00 0.00 0.00 4.85
3380 4467 0.329596 ACTGCATTCCAGGAGTTCCC 59.670 55.000 0.00 0.00 46.14 3.97
3396 4483 3.815407 AAGGGGCTGCCAACCACTG 62.815 63.158 22.05 0.00 41.24 3.66
3397 4484 3.511610 AAGGGGCTGCCAACCACT 61.512 61.111 22.05 7.11 45.20 4.00
3408 4495 1.308998 CGACATTATGACCAAGGGGC 58.691 55.000 0.00 0.00 37.90 5.80
3414 4501 2.746904 CAGTTTGCCGACATTATGACCA 59.253 45.455 0.00 0.00 0.00 4.02
3415 4502 2.747446 ACAGTTTGCCGACATTATGACC 59.253 45.455 0.00 0.00 0.00 4.02
3428 4515 0.872388 CCGACTACCCAACAGTTTGC 59.128 55.000 0.00 0.00 0.00 3.68
3461 4548 0.868406 GTTCAGTTGGGTCAGCTTCG 59.132 55.000 0.00 0.00 0.00 3.79
3504 4591 3.678072 ACACACCAAACATATCGAACTCG 59.322 43.478 0.00 0.00 41.45 4.18
3507 4594 7.302524 ACATAAACACACCAAACATATCGAAC 58.697 34.615 0.00 0.00 0.00 3.95
3511 4598 6.865726 TGCAACATAAACACACCAAACATATC 59.134 34.615 0.00 0.00 0.00 1.63
3539 4626 0.179018 ACCTATCTTGCGGCCAATCC 60.179 55.000 2.24 0.00 0.00 3.01
3544 4631 2.902343 GCCACCTATCTTGCGGCC 60.902 66.667 0.00 0.00 36.73 6.13
3546 4633 2.587322 TTCGGCCACCTATCTTGCGG 62.587 60.000 2.24 0.00 0.00 5.69
3560 4647 7.591426 GGTGATCTTTTATGATAATGTTTCGGC 59.409 37.037 0.00 0.00 0.00 5.54
3571 4658 5.552870 AGGCTACGGTGATCTTTTATGAT 57.447 39.130 0.00 0.00 0.00 2.45
3574 4661 4.369182 CGAAGGCTACGGTGATCTTTTAT 58.631 43.478 0.00 0.00 0.00 1.40
3575 4662 3.429822 CCGAAGGCTACGGTGATCTTTTA 60.430 47.826 0.00 0.00 46.14 1.52
3577 4664 1.134788 CCGAAGGCTACGGTGATCTTT 60.135 52.381 0.00 0.00 46.14 2.52
3580 4667 4.732106 CCGAAGGCTACGGTGATC 57.268 61.111 0.00 0.00 46.14 2.92
3602 4689 3.753294 TCTTGGTGAACTTCTGGTCTC 57.247 47.619 0.00 0.00 0.00 3.36
3624 4711 0.586802 GACTTCTTGGTTGCGTCACC 59.413 55.000 0.00 0.00 37.34 4.02
3632 4719 2.156343 GTCGCTGAGACTTCTTGGTT 57.844 50.000 4.18 0.00 46.13 3.67
3633 4720 3.896317 GTCGCTGAGACTTCTTGGT 57.104 52.632 4.18 0.00 46.13 3.67


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

AutoCloner maintained by Alex Coulton.