Multiple sequence alignment - TraesCS6B01G293400

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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 TraesCS6B01G293400 chr6B 100.000 2852 0 0 1 2852 526828038 526830889 0.000000e+00 5267
1 TraesCS6B01G293400 chr6B 94.962 655 30 3 1 653 159003689 159003036 0.000000e+00 1024
2 TraesCS6B01G293400 chr6B 96.859 382 11 1 654 1034 179072647 179072266 3.100000e-179 638
3 TraesCS6B01G293400 chr4B 89.128 1021 98 12 22 1034 586664774 586663759 0.000000e+00 1258
4 TraesCS6B01G293400 chr4B 94.977 657 29 4 1 654 28872120 28871465 0.000000e+00 1027
5 TraesCS6B01G293400 chr4B 74.775 1332 298 34 1508 2821 56256083 56257394 5.330000e-157 564
6 TraesCS6B01G293400 chr1B 87.488 1047 110 16 1 1034 105412159 105411121 0.000000e+00 1188
7 TraesCS6B01G293400 chr7B 95.260 654 28 2 1 653 505487969 505488620 0.000000e+00 1033
8 TraesCS6B01G293400 chr7B 95.253 653 29 2 1 653 505493432 505494082 0.000000e+00 1033
9 TraesCS6B01G293400 chr7B 76.415 1802 391 28 1035 2823 591583097 591584877 0.000000e+00 942
10 TraesCS6B01G293400 chr7B 77.559 762 149 18 2056 2808 181029120 181028372 9.380000e-120 440
11 TraesCS6B01G293400 chr3B 95.100 653 30 1 1 653 727625383 727626033 0.000000e+00 1027
12 TraesCS6B01G293400 chr3B 94.962 655 31 1 1 653 106375366 106376020 0.000000e+00 1026
13 TraesCS6B01G293400 chr3B 85.419 1015 116 12 28 1035 639807379 639806390 0.000000e+00 1026
14 TraesCS6B01G293400 chr3B 94.436 665 33 4 1 664 71046651 71047312 0.000000e+00 1020
15 TraesCS6B01G293400 chr7D 84.976 1045 120 28 1 1035 76246947 76247964 0.000000e+00 1026
16 TraesCS6B01G293400 chr7D 96.850 381 12 0 654 1034 108026268 108025888 3.100000e-179 638
17 TraesCS6B01G293400 chr7D 78.997 738 141 10 2088 2818 476781780 476781050 2.550000e-135 492
18 TraesCS6B01G293400 chr1D 76.637 1802 362 39 1035 2821 126973443 126975200 0.000000e+00 941
19 TraesCS6B01G293400 chr6A 83.093 1041 133 31 1 1028 493257275 493256265 0.000000e+00 907
20 TraesCS6B01G293400 chr6A 77.056 754 161 12 2058 2805 3678838 3679585 9.450000e-115 424
21 TraesCS6B01G293400 chr6A 75.255 687 154 15 2058 2736 532538056 532538734 2.130000e-81 313
22 TraesCS6B01G293400 chr3D 84.683 914 101 18 128 1034 351608142 351607261 0.000000e+00 876
23 TraesCS6B01G293400 chr3D 76.448 777 157 23 2056 2819 46195658 46194895 5.730000e-107 398
24 TraesCS6B01G293400 chr3D 76.558 738 163 8 2076 2809 450973068 450973799 2.060000e-106 396
25 TraesCS6B01G293400 chr3D 74.545 770 170 25 2052 2808 551590022 551589266 2.130000e-81 313
26 TraesCS6B01G293400 chr5A 97.113 381 11 0 654 1034 665383299 665382919 0.000000e+00 643
27 TraesCS6B01G293400 chr5D 96.850 381 12 0 654 1034 96017025 96016645 3.100000e-179 638
28 TraesCS6B01G293400 chr5D 75.653 727 163 12 2086 2805 349364487 349363768 1.630000e-92 350
29 TraesCS6B01G293400 chr5D 75.824 637 133 13 2058 2691 13918253 13918871 1.280000e-78 303
30 TraesCS6B01G293400 chr2A 79.095 751 136 17 2092 2832 704974 705713 5.490000e-137 497
31 TraesCS6B01G293400 chr2A 79.095 751 136 17 2092 2832 710545 711284 5.490000e-137 497
32 TraesCS6B01G293400 chr4D 77.038 736 142 16 2079 2808 46411047 46410333 5.730000e-107 398
33 TraesCS6B01G293400 chr4D 77.847 483 99 8 2076 2554 449222379 449221901 2.780000e-75 292
34 TraesCS6B01G293400 chr4D 80.678 295 53 4 2058 2350 208551407 208551699 2.860000e-55 226
35 TraesCS6B01G293400 chr7A 76.036 772 169 16 2056 2820 316035641 316034879 1.240000e-103 387
36 TraesCS6B01G293400 chr7A 75.736 713 155 18 2114 2817 680625125 680624422 2.720000e-90 342
37 TraesCS6B01G293400 chr4A 76.146 742 164 11 2076 2811 552513054 552513788 7.460000e-101 377
38 TraesCS6B01G293400 chr1A 74.902 769 166 23 2056 2811 280480036 280480790 2.740000e-85 326
39 TraesCS6B01G293400 chr1A 73.997 773 182 18 2056 2819 253038500 253039262 2.150000e-76 296
40 TraesCS6B01G293400 chrUn 83.190 232 33 5 2119 2347 29538068 29537840 1.040000e-49 207


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 TraesCS6B01G293400 chr6B 526828038 526830889 2851 False 5267 5267 100.000 1 2852 1 chr6B.!!$F1 2851
1 TraesCS6B01G293400 chr6B 159003036 159003689 653 True 1024 1024 94.962 1 653 1 chr6B.!!$R1 652
2 TraesCS6B01G293400 chr4B 586663759 586664774 1015 True 1258 1258 89.128 22 1034 1 chr4B.!!$R2 1012
3 TraesCS6B01G293400 chr4B 28871465 28872120 655 True 1027 1027 94.977 1 654 1 chr4B.!!$R1 653
4 TraesCS6B01G293400 chr4B 56256083 56257394 1311 False 564 564 74.775 1508 2821 1 chr4B.!!$F1 1313
5 TraesCS6B01G293400 chr1B 105411121 105412159 1038 True 1188 1188 87.488 1 1034 1 chr1B.!!$R1 1033
6 TraesCS6B01G293400 chr7B 505487969 505488620 651 False 1033 1033 95.260 1 653 1 chr7B.!!$F1 652
7 TraesCS6B01G293400 chr7B 505493432 505494082 650 False 1033 1033 95.253 1 653 1 chr7B.!!$F2 652
8 TraesCS6B01G293400 chr7B 591583097 591584877 1780 False 942 942 76.415 1035 2823 1 chr7B.!!$F3 1788
9 TraesCS6B01G293400 chr7B 181028372 181029120 748 True 440 440 77.559 2056 2808 1 chr7B.!!$R1 752
10 TraesCS6B01G293400 chr3B 727625383 727626033 650 False 1027 1027 95.100 1 653 1 chr3B.!!$F3 652
11 TraesCS6B01G293400 chr3B 106375366 106376020 654 False 1026 1026 94.962 1 653 1 chr3B.!!$F2 652
12 TraesCS6B01G293400 chr3B 639806390 639807379 989 True 1026 1026 85.419 28 1035 1 chr3B.!!$R1 1007
13 TraesCS6B01G293400 chr3B 71046651 71047312 661 False 1020 1020 94.436 1 664 1 chr3B.!!$F1 663
14 TraesCS6B01G293400 chr7D 76246947 76247964 1017 False 1026 1026 84.976 1 1035 1 chr7D.!!$F1 1034
15 TraesCS6B01G293400 chr7D 476781050 476781780 730 True 492 492 78.997 2088 2818 1 chr7D.!!$R2 730
16 TraesCS6B01G293400 chr1D 126973443 126975200 1757 False 941 941 76.637 1035 2821 1 chr1D.!!$F1 1786
17 TraesCS6B01G293400 chr6A 493256265 493257275 1010 True 907 907 83.093 1 1028 1 chr6A.!!$R1 1027
18 TraesCS6B01G293400 chr6A 3678838 3679585 747 False 424 424 77.056 2058 2805 1 chr6A.!!$F1 747
19 TraesCS6B01G293400 chr6A 532538056 532538734 678 False 313 313 75.255 2058 2736 1 chr6A.!!$F2 678
20 TraesCS6B01G293400 chr3D 351607261 351608142 881 True 876 876 84.683 128 1034 1 chr3D.!!$R2 906
21 TraesCS6B01G293400 chr3D 46194895 46195658 763 True 398 398 76.448 2056 2819 1 chr3D.!!$R1 763
22 TraesCS6B01G293400 chr3D 450973068 450973799 731 False 396 396 76.558 2076 2809 1 chr3D.!!$F1 733
23 TraesCS6B01G293400 chr3D 551589266 551590022 756 True 313 313 74.545 2052 2808 1 chr3D.!!$R3 756
24 TraesCS6B01G293400 chr5D 349363768 349364487 719 True 350 350 75.653 2086 2805 1 chr5D.!!$R2 719
25 TraesCS6B01G293400 chr5D 13918253 13918871 618 False 303 303 75.824 2058 2691 1 chr5D.!!$F1 633
26 TraesCS6B01G293400 chr2A 704974 705713 739 False 497 497 79.095 2092 2832 1 chr2A.!!$F1 740
27 TraesCS6B01G293400 chr2A 710545 711284 739 False 497 497 79.095 2092 2832 1 chr2A.!!$F2 740
28 TraesCS6B01G293400 chr4D 46410333 46411047 714 True 398 398 77.038 2079 2808 1 chr4D.!!$R1 729
29 TraesCS6B01G293400 chr7A 316034879 316035641 762 True 387 387 76.036 2056 2820 1 chr7A.!!$R1 764
30 TraesCS6B01G293400 chr7A 680624422 680625125 703 True 342 342 75.736 2114 2817 1 chr7A.!!$R2 703
31 TraesCS6B01G293400 chr4A 552513054 552513788 734 False 377 377 76.146 2076 2811 1 chr4A.!!$F1 735
32 TraesCS6B01G293400 chr1A 280480036 280480790 754 False 326 326 74.902 2056 2811 1 chr1A.!!$F2 755
33 TraesCS6B01G293400 chr1A 253038500 253039262 762 False 296 296 73.997 2056 2819 1 chr1A.!!$F1 763

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
444 459 2.078392 TCCAAAAATAACGCTCCCGAC 58.922 47.619 0.00 0.0 38.29 4.79 F
1306 1328 0.455410 TATGCATTTGCCGCCAAGAC 59.545 50.000 3.54 0.0 41.18 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1576 1598 0.031111 TCCCCATTCTCGTCCCTGAT 60.031 55.0 0.0 0.0 0.00 2.90 R
2574 2602 0.179084 TTGAGCGATCCCGATGAACC 60.179 55.0 0.0 0.0 38.22 3.62 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
67 68 3.756117 TCCAAAAAGAGAGAAGAAGCCC 58.244 45.455 0.00 0.00 0.00 5.19
82 83 5.799827 AGAAGCCCTCTAGCTAATAACTG 57.200 43.478 0.00 0.00 44.11 3.16
125 126 5.407407 AAACTACTCACAACTCATCGGAT 57.593 39.130 0.00 0.00 0.00 4.18
444 459 2.078392 TCCAAAAATAACGCTCCCGAC 58.922 47.619 0.00 0.00 38.29 4.79
755 777 2.199236 GCTGTTAACGGGTTATCGGAG 58.801 52.381 16.13 0.00 0.00 4.63
769 791 2.114411 GGAGCCAAAACCCGACCA 59.886 61.111 0.00 0.00 0.00 4.02
853 875 3.224884 TCTGTGACGCACGATTTATCA 57.775 42.857 0.00 0.00 37.14 2.15
1047 1069 4.601406 TTGTAGTGCCCCCAATAATCTT 57.399 40.909 0.00 0.00 0.00 2.40
1053 1075 3.706086 GTGCCCCCAATAATCTTCACATT 59.294 43.478 0.00 0.00 0.00 2.71
1056 1078 4.038402 GCCCCCAATAATCTTCACATTCAG 59.962 45.833 0.00 0.00 0.00 3.02
1076 1098 2.777109 CGATCTCGTCAGCGATGAC 58.223 57.895 23.45 23.45 46.80 3.06
1112 1134 1.154338 CGAAAGGCTTGCTGCTTCG 60.154 57.895 0.00 0.83 40.87 3.79
1113 1135 1.845809 CGAAAGGCTTGCTGCTTCGT 61.846 55.000 0.00 0.00 41.42 3.85
1117 1139 2.359230 GCTTGCTGCTTCGTCCCT 60.359 61.111 0.00 0.00 38.95 4.20
1122 1144 4.148825 CTGCTTCGTCCCTCGGGG 62.149 72.222 0.00 0.00 46.11 5.73
1137 1159 3.118186 CCTCGGGGGATAATGTGTTTGTA 60.118 47.826 0.00 0.00 37.23 2.41
1146 1168 7.196331 GGGATAATGTGTTTGTAGCTGAATTC 58.804 38.462 0.00 0.00 0.00 2.17
1149 1171 3.472652 TGTGTTTGTAGCTGAATTCGGT 58.527 40.909 15.63 10.86 0.00 4.69
1153 1175 2.973694 TGTAGCTGAATTCGGTACCC 57.026 50.000 23.78 8.58 35.18 3.69
1158 1180 0.541863 CTGAATTCGGTACCCAGGCT 59.458 55.000 6.25 0.00 0.00 4.58
1161 1183 1.141053 GAATTCGGTACCCAGGCTGAT 59.859 52.381 17.94 6.25 0.00 2.90
1164 1186 0.469331 TCGGTACCCAGGCTGATAGG 60.469 60.000 17.94 11.55 0.00 2.57
1165 1187 0.759436 CGGTACCCAGGCTGATAGGT 60.759 60.000 17.94 17.08 36.36 3.08
1174 1196 0.691078 GGCTGATAGGTCCAGGGTGA 60.691 60.000 0.00 0.00 32.51 4.02
1182 1204 1.265454 GGTCCAGGGTGATCGAAGGT 61.265 60.000 0.00 0.00 0.00 3.50
1185 1207 0.905357 CCAGGGTGATCGAAGGTTCT 59.095 55.000 0.00 0.00 0.00 3.01
1208 1230 3.364549 CATGGATGGTGGGTAAACATGT 58.635 45.455 0.00 0.00 32.01 3.21
1209 1231 3.534357 TGGATGGTGGGTAAACATGTT 57.466 42.857 4.92 4.92 0.00 2.71
1215 1237 2.364002 GGTGGGTAAACATGTTGTGCTT 59.636 45.455 12.82 0.00 0.00 3.91
1218 1240 3.568007 TGGGTAAACATGTTGTGCTTCTC 59.432 43.478 12.82 0.00 0.00 2.87
1224 1246 2.620115 ACATGTTGTGCTTCTCAAGGTG 59.380 45.455 0.00 0.00 0.00 4.00
1231 1253 3.953612 TGTGCTTCTCAAGGTGTTTGATT 59.046 39.130 0.00 0.00 44.48 2.57
1234 1256 4.202141 TGCTTCTCAAGGTGTTTGATTTGG 60.202 41.667 0.00 0.00 44.48 3.28
1239 1261 5.598005 TCTCAAGGTGTTTGATTTGGATGTT 59.402 36.000 0.00 0.00 44.48 2.71
1251 1273 5.832595 TGATTTGGATGTTCAACCTCTTCAA 59.167 36.000 1.20 0.00 0.00 2.69
1254 1276 5.560722 TGGATGTTCAACCTCTTCAAGTA 57.439 39.130 1.20 0.00 0.00 2.24
1257 1279 5.763204 GGATGTTCAACCTCTTCAAGTACAA 59.237 40.000 0.00 0.00 0.00 2.41
1261 1283 8.062065 TGTTCAACCTCTTCAAGTACAATTTT 57.938 30.769 0.00 0.00 0.00 1.82
1266 1288 7.073342 ACCTCTTCAAGTACAATTTTATCGC 57.927 36.000 0.00 0.00 0.00 4.58
1275 1297 5.825679 AGTACAATTTTATCGCTTGGCCATA 59.174 36.000 6.09 0.00 0.00 2.74
1293 1315 2.495155 TATGGGCTCGCATTATGCAT 57.505 45.000 17.75 3.79 45.36 3.96
1299 1321 1.401530 CTCGCATTATGCATTTGCCG 58.598 50.000 21.70 17.63 45.36 5.69
1306 1328 0.455410 TATGCATTTGCCGCCAAGAC 59.545 50.000 3.54 0.00 41.18 3.01
1308 1330 1.290009 GCATTTGCCGCCAAGACTT 59.710 52.632 0.00 0.00 34.31 3.01
1316 1338 1.017387 CCGCCAAGACTTATGAAGGC 58.983 55.000 3.88 3.88 38.73 4.35
1317 1339 1.017387 CGCCAAGACTTATGAAGGCC 58.983 55.000 0.00 0.00 37.17 5.19
1338 1360 1.474330 AACTTGGGATGGAATTCGCC 58.526 50.000 0.00 0.87 0.00 5.54
1344 1366 0.459899 GGATGGAATTCGCCAAACCC 59.540 55.000 0.00 0.00 42.16 4.11
1347 1369 2.516227 TGGAATTCGCCAAACCCATA 57.484 45.000 0.00 0.00 34.31 2.74
1362 1384 0.764890 CCATAGGGCGGATCTCCAAA 59.235 55.000 6.83 0.00 35.14 3.28
1383 1405 2.508716 AGTGGAATCTCATGCAGATGGT 59.491 45.455 7.99 0.00 41.47 3.55
1395 1417 4.864334 GATGGTCGCTGCTGGGGG 62.864 72.222 7.80 0.00 0.00 5.40
1407 1429 1.050988 GCTGGGGGAGCTACATGAGA 61.051 60.000 0.00 0.00 45.21 3.27
1415 1437 3.550820 GGAGCTACATGAGAGTGAGAGA 58.449 50.000 0.00 0.00 0.00 3.10
1428 1450 4.467082 AGAGTGAGAGATGAGATTGCTGTT 59.533 41.667 0.00 0.00 0.00 3.16
1431 1453 4.934001 GTGAGAGATGAGATTGCTGTTCAA 59.066 41.667 0.00 0.00 39.32 2.69
1434 1456 5.802465 AGAGATGAGATTGCTGTTCAAGAA 58.198 37.500 0.00 0.00 38.22 2.52
1438 1460 2.154462 AGATTGCTGTTCAAGAACCGG 58.846 47.619 0.00 0.00 40.46 5.28
1440 1462 1.757682 TTGCTGTTCAAGAACCGGTT 58.242 45.000 22.50 22.50 40.46 4.44
1458 1480 3.121126 CGGTTGTTCGTTATGTGACAGTC 60.121 47.826 0.00 0.00 0.00 3.51
1475 1497 4.051922 ACAGTCACTTTCGTAAAGCTCAG 58.948 43.478 7.10 0.00 42.27 3.35
1481 1503 6.586844 GTCACTTTCGTAAAGCTCAGAACTAT 59.413 38.462 7.10 0.00 42.27 2.12
1482 1504 6.586463 TCACTTTCGTAAAGCTCAGAACTATG 59.414 38.462 7.10 0.00 42.27 2.23
1483 1505 6.586463 CACTTTCGTAAAGCTCAGAACTATGA 59.414 38.462 7.10 0.00 42.27 2.15
1494 1516 7.671302 AGCTCAGAACTATGAAAACTTACTCA 58.329 34.615 0.00 0.00 0.00 3.41
1506 1528 9.725019 ATGAAAACTTACTCAGTGATGTATGAA 57.275 29.630 15.84 1.98 35.12 2.57
1512 1534 3.055819 ACTCAGTGATGTATGAACGGCTT 60.056 43.478 0.00 0.00 0.00 4.35
1515 1537 2.501723 AGTGATGTATGAACGGCTTCCT 59.498 45.455 0.00 0.00 0.00 3.36
1518 1540 3.938963 TGATGTATGAACGGCTTCCTTTC 59.061 43.478 0.00 0.00 33.19 2.62
1519 1541 3.695830 TGTATGAACGGCTTCCTTTCT 57.304 42.857 4.17 0.00 33.65 2.52
1523 1545 5.419788 TGTATGAACGGCTTCCTTTCTACTA 59.580 40.000 4.17 0.00 33.65 1.82
1524 1546 5.615925 ATGAACGGCTTCCTTTCTACTAT 57.384 39.130 4.17 0.00 33.65 2.12
1536 1558 5.425539 TCCTTTCTACTATTTCTCCTGTGGG 59.574 44.000 0.00 0.00 0.00 4.61
1537 1559 4.755266 TTCTACTATTTCTCCTGTGGGC 57.245 45.455 0.00 0.00 0.00 5.36
1542 1564 2.270434 ATTTCTCCTGTGGGCTCCTA 57.730 50.000 0.00 0.00 0.00 2.94
1545 1567 1.002274 CTCCTGTGGGCTCCTAGGT 59.998 63.158 9.08 0.00 32.90 3.08
1548 1570 0.692419 CCTGTGGGCTCCTAGGTCAT 60.692 60.000 9.08 0.00 0.00 3.06
1551 1573 0.470341 GTGGGCTCCTAGGTCATTCC 59.530 60.000 9.08 5.66 0.00 3.01
1554 1576 1.692762 GGGCTCCTAGGTCATTCCTCA 60.693 57.143 9.08 0.00 44.42 3.86
1558 1580 3.244387 GCTCCTAGGTCATTCCTCAATCC 60.244 52.174 9.08 0.00 44.42 3.01
1560 1582 4.635473 TCCTAGGTCATTCCTCAATCCTT 58.365 43.478 9.08 0.00 44.42 3.36
1563 1585 4.664688 AGGTCATTCCTCAATCCTTTGT 57.335 40.909 0.00 0.00 44.42 2.83
1566 1588 4.335416 GTCATTCCTCAATCCTTTGTCCA 58.665 43.478 0.00 0.00 34.32 4.02
1568 1590 4.766891 TCATTCCTCAATCCTTTGTCCAAC 59.233 41.667 0.00 0.00 34.32 3.77
1576 1598 1.228124 CTTTGTCCAACTCCGGGCA 60.228 57.895 0.00 0.00 39.45 5.36
1581 1603 2.124570 CCAACTCCGGGCATCAGG 60.125 66.667 0.00 0.00 0.00 3.86
1584 1606 2.670148 AACTCCGGGCATCAGGGAC 61.670 63.158 0.00 0.00 0.00 4.46
1587 1609 4.227134 CCGGGCATCAGGGACGAG 62.227 72.222 0.00 0.00 0.00 4.18
1609 1631 4.567318 GGGACCTGCCTTATGCTG 57.433 61.111 0.00 0.00 42.00 4.41
1617 1639 2.159282 CCTGCCTTATGCTGCAAAGAAG 60.159 50.000 19.25 16.09 42.00 2.85
1629 1651 2.105323 CAAAGAAGTTGCGTGTGACC 57.895 50.000 0.00 0.00 0.00 4.02
1631 1653 1.157870 AAGAAGTTGCGTGTGACCGG 61.158 55.000 0.00 0.00 0.00 5.28
1634 1656 2.581208 AAGTTGCGTGTGACCGGTGA 62.581 55.000 14.63 0.00 0.00 4.02
1635 1657 1.959226 GTTGCGTGTGACCGGTGAT 60.959 57.895 14.63 0.00 0.00 3.06
1636 1658 1.227704 TTGCGTGTGACCGGTGATT 60.228 52.632 14.63 0.00 0.00 2.57
1638 1660 0.668096 TGCGTGTGACCGGTGATTAC 60.668 55.000 14.63 6.58 0.00 1.89
1639 1661 0.389426 GCGTGTGACCGGTGATTACT 60.389 55.000 14.63 0.00 0.00 2.24
1640 1662 1.938016 GCGTGTGACCGGTGATTACTT 60.938 52.381 14.63 0.00 0.00 2.24
1647 1669 3.056107 TGACCGGTGATTACTTGAGGAAG 60.056 47.826 14.63 0.00 35.07 3.46
1650 1672 3.056107 CCGGTGATTACTTGAGGAAGTCA 60.056 47.826 0.00 0.00 41.75 3.41
1653 1675 4.020128 GGTGATTACTTGAGGAAGTCAGGT 60.020 45.833 0.00 0.00 46.70 4.00
1656 1678 2.103153 ACTTGAGGAAGTCAGGTGGA 57.897 50.000 0.00 0.00 43.60 4.02
1659 1681 1.186200 TGAGGAAGTCAGGTGGATCG 58.814 55.000 0.00 0.00 0.00 3.69
1665 1687 2.223803 AGTCAGGTGGATCGAAGTCT 57.776 50.000 0.00 0.00 0.00 3.24
1668 1690 2.025155 TCAGGTGGATCGAAGTCTAGC 58.975 52.381 0.00 0.00 0.00 3.42
1678 1700 4.063998 TCGAAGTCTAGCAATGCATCAT 57.936 40.909 8.35 0.00 0.00 2.45
1680 1702 3.805971 CGAAGTCTAGCAATGCATCATCA 59.194 43.478 8.35 0.00 0.00 3.07
1683 1705 3.995048 AGTCTAGCAATGCATCATCATCG 59.005 43.478 8.35 0.00 0.00 3.84
1686 1708 0.312729 GCAATGCATCATCATCGGCA 59.687 50.000 0.00 0.00 41.00 5.69
1688 1710 0.596577 AATGCATCATCATCGGCAGC 59.403 50.000 0.00 0.00 39.95 5.25
1692 1714 0.534427 CATCATCATCGGCAGCTGGT 60.534 55.000 17.12 0.00 0.00 4.00
1696 1718 1.332889 ATCATCGGCAGCTGGTGAGA 61.333 55.000 21.85 9.29 0.00 3.27
1697 1719 1.521010 CATCGGCAGCTGGTGAGAG 60.521 63.158 17.12 0.84 0.00 3.20
1698 1720 1.986757 ATCGGCAGCTGGTGAGAGT 60.987 57.895 17.12 0.00 0.00 3.24
1702 1724 0.321671 GGCAGCTGGTGAGAGTAACA 59.678 55.000 17.12 0.00 0.00 2.41
1706 1728 3.619038 GCAGCTGGTGAGAGTAACAATAC 59.381 47.826 17.12 0.00 0.00 1.89
1709 1731 4.772624 AGCTGGTGAGAGTAACAATACTGA 59.227 41.667 0.00 0.00 42.47 3.41
1716 1738 5.125578 TGAGAGTAACAATACTGATGCTCGT 59.874 40.000 0.00 0.00 42.47 4.18
1717 1739 5.344066 AGAGTAACAATACTGATGCTCGTG 58.656 41.667 0.00 0.00 42.47 4.35
1718 1740 5.073311 AGTAACAATACTGATGCTCGTGT 57.927 39.130 0.00 0.00 40.88 4.49
1719 1741 4.864806 AGTAACAATACTGATGCTCGTGTG 59.135 41.667 0.00 0.00 40.88 3.82
1720 1742 2.002586 ACAATACTGATGCTCGTGTGC 58.997 47.619 0.00 0.00 0.00 4.57
1725 1747 0.390866 CTGATGCTCGTGTGCCTTCT 60.391 55.000 0.00 0.00 0.00 2.85
1729 1751 0.601046 TGCTCGTGTGCCTTCTTCAG 60.601 55.000 0.00 0.00 0.00 3.02
1737 1759 3.068881 CCTTCTTCAGGCCGACCA 58.931 61.111 0.00 0.00 39.06 4.02
1741 1763 0.250727 TTCTTCAGGCCGACCAAAGG 60.251 55.000 0.00 0.00 39.06 3.11
1752 1774 1.804746 CGACCAAAGGCCAAAAACCAC 60.805 52.381 5.01 0.00 0.00 4.16
1770 1792 0.035458 ACACAGGTTCTGCTAGTGGC 59.965 55.000 0.00 0.00 42.22 5.01
1773 1795 0.737715 CAGGTTCTGCTAGTGGCGAC 60.738 60.000 0.00 0.00 45.43 5.19
1799 1821 1.138661 GGTGCCATCTCCTCTCAAGAG 59.861 57.143 0.00 0.00 41.71 2.85
1825 1847 0.613777 GGGGTTCTTCTCATGGACGT 59.386 55.000 0.00 0.00 0.00 4.34
1828 1850 1.002087 GGTTCTTCTCATGGACGTGGT 59.998 52.381 0.00 0.00 0.00 4.16
1831 1853 0.458543 CTTCTCATGGACGTGGTCGG 60.459 60.000 0.00 0.00 41.85 4.79
1860 1882 4.789123 CCGTGGTAAAGGGCGGGG 62.789 72.222 0.00 0.00 40.45 5.73
1863 1885 4.354162 TGGTAAAGGGCGGGGTGC 62.354 66.667 0.00 0.00 45.38 5.01
1866 1888 2.931105 TAAAGGGCGGGGTGCTGA 60.931 61.111 0.00 0.00 45.43 4.26
1867 1889 2.305607 TAAAGGGCGGGGTGCTGAT 61.306 57.895 0.00 0.00 45.43 2.90
1868 1890 2.265467 TAAAGGGCGGGGTGCTGATC 62.265 60.000 0.00 0.00 45.43 2.92
1876 1898 1.742768 GGGTGCTGATCCGAGTAGG 59.257 63.158 0.00 0.00 42.97 3.18
1885 1907 3.170717 TGATCCGAGTAGGGAGTTGTTT 58.829 45.455 0.00 0.00 40.02 2.83
1888 1910 2.561419 TCCGAGTAGGGAGTTGTTTCTG 59.439 50.000 0.00 0.00 41.52 3.02
1891 1913 3.508793 CGAGTAGGGAGTTGTTTCTGGTA 59.491 47.826 0.00 0.00 0.00 3.25
1905 1928 7.083875 TGTTTCTGGTACAACAAAAGAAGAG 57.916 36.000 0.00 0.00 38.70 2.85
1906 1929 5.751243 TTCTGGTACAACAAAAGAAGAGC 57.249 39.130 0.00 0.00 38.70 4.09
1915 1938 3.391049 ACAAAAGAAGAGCAGTACGACC 58.609 45.455 0.00 0.00 0.00 4.79
1918 1941 0.608582 AGAAGAGCAGTACGACCGGT 60.609 55.000 6.92 6.92 0.00 5.28
1932 1955 2.353803 CGACCGGTCAGAAGAGGAAATT 60.354 50.000 32.80 0.00 0.00 1.82
1939 1962 5.163814 CGGTCAGAAGAGGAAATTTGCTAAG 60.164 44.000 12.63 1.71 0.00 2.18
1941 1964 5.940470 GTCAGAAGAGGAAATTTGCTAAGGA 59.060 40.000 12.63 3.94 0.00 3.36
1949 1972 4.488879 GAAATTTGCTAAGGACCAAGCTG 58.511 43.478 17.04 0.00 39.53 4.24
1950 1973 2.656947 TTTGCTAAGGACCAAGCTGT 57.343 45.000 17.04 0.00 39.53 4.40
1954 1977 1.270839 GCTAAGGACCAAGCTGTGACA 60.271 52.381 10.75 0.00 35.80 3.58
1955 1978 2.616510 GCTAAGGACCAAGCTGTGACAT 60.617 50.000 10.75 0.00 35.80 3.06
1956 1979 2.664402 AAGGACCAAGCTGTGACATT 57.336 45.000 0.00 0.00 0.00 2.71
1959 1982 2.158623 AGGACCAAGCTGTGACATTGAA 60.159 45.455 0.74 0.00 0.00 2.69
1960 1983 2.821969 GGACCAAGCTGTGACATTGAAT 59.178 45.455 0.74 0.00 0.00 2.57
1961 1984 3.256631 GGACCAAGCTGTGACATTGAATT 59.743 43.478 0.74 0.00 0.00 2.17
1962 1985 4.479619 GACCAAGCTGTGACATTGAATTC 58.520 43.478 0.00 0.00 0.00 2.17
1966 1989 3.087031 AGCTGTGACATTGAATTCTGGG 58.913 45.455 7.05 0.00 0.00 4.45
1967 1990 3.084039 GCTGTGACATTGAATTCTGGGA 58.916 45.455 7.05 0.00 0.00 4.37
1968 1991 3.128242 GCTGTGACATTGAATTCTGGGAG 59.872 47.826 7.05 0.00 0.00 4.30
1970 1993 5.491070 CTGTGACATTGAATTCTGGGAGTA 58.509 41.667 7.05 0.00 0.00 2.59
1971 1994 5.245531 TGTGACATTGAATTCTGGGAGTAC 58.754 41.667 7.05 0.00 0.00 2.73
1973 1996 5.882557 GTGACATTGAATTCTGGGAGTACAT 59.117 40.000 7.05 0.00 0.00 2.29
1974 1997 5.882000 TGACATTGAATTCTGGGAGTACATG 59.118 40.000 7.05 0.00 0.00 3.21
1976 1999 3.931907 TGAATTCTGGGAGTACATGGG 57.068 47.619 7.05 0.00 0.00 4.00
1977 2000 3.459828 TGAATTCTGGGAGTACATGGGA 58.540 45.455 7.05 0.00 0.00 4.37
1978 2001 3.455910 TGAATTCTGGGAGTACATGGGAG 59.544 47.826 7.05 0.00 0.00 4.30
1985 2008 2.173569 GGGAGTACATGGGAGAATGCTT 59.826 50.000 0.00 0.00 0.00 3.91
1987 2010 3.629398 GGAGTACATGGGAGAATGCTTTG 59.371 47.826 0.00 0.00 0.00 2.77
1990 2013 1.272872 ACATGGGAGAATGCTTTGGCT 60.273 47.619 0.00 0.00 39.59 4.75
1993 2016 1.076024 TGGGAGAATGCTTTGGCTCTT 59.924 47.619 0.00 0.00 39.59 2.85
1996 2019 2.560105 GGAGAATGCTTTGGCTCTTGTT 59.440 45.455 0.00 0.00 39.59 2.83
1999 2022 1.260544 ATGCTTTGGCTCTTGTTCCC 58.739 50.000 0.00 0.00 39.59 3.97
2005 2028 0.321671 TGGCTCTTGTTCCCTCTTCG 59.678 55.000 0.00 0.00 0.00 3.79
2006 2029 0.608640 GGCTCTTGTTCCCTCTTCGA 59.391 55.000 0.00 0.00 0.00 3.71
2008 2031 1.273886 GCTCTTGTTCCCTCTTCGAGT 59.726 52.381 0.00 0.00 0.00 4.18
2010 2033 1.000955 TCTTGTTCCCTCTTCGAGTGC 59.999 52.381 0.00 0.00 0.00 4.40
2016 2039 0.967887 CCCTCTTCGAGTGCTCCTGA 60.968 60.000 0.00 0.00 0.00 3.86
2017 2040 1.110442 CCTCTTCGAGTGCTCCTGAT 58.890 55.000 0.00 0.00 0.00 2.90
2019 2042 1.476085 CTCTTCGAGTGCTCCTGATGT 59.524 52.381 0.00 0.00 0.00 3.06
2022 2045 1.098869 TCGAGTGCTCCTGATGTCTC 58.901 55.000 0.00 0.00 0.00 3.36
2023 2046 1.102154 CGAGTGCTCCTGATGTCTCT 58.898 55.000 0.00 0.00 0.00 3.10
2024 2047 1.202279 CGAGTGCTCCTGATGTCTCTG 60.202 57.143 0.00 0.00 0.00 3.35
2025 2048 2.098614 GAGTGCTCCTGATGTCTCTGA 58.901 52.381 0.00 0.00 0.00 3.27
2026 2049 2.099592 GAGTGCTCCTGATGTCTCTGAG 59.900 54.545 0.00 0.00 0.00 3.35
2028 2051 1.272928 TGCTCCTGATGTCTCTGAGGT 60.273 52.381 4.59 0.00 0.00 3.85
2029 2052 1.830477 GCTCCTGATGTCTCTGAGGTT 59.170 52.381 4.59 0.00 0.00 3.50
2039 2062 1.433199 TCTCTGAGGTTGGGGAGAAGA 59.567 52.381 4.59 0.00 32.76 2.87
2040 2063 1.552792 CTCTGAGGTTGGGGAGAAGAC 59.447 57.143 0.00 0.00 0.00 3.01
2042 2065 0.104672 TGAGGTTGGGGAGAAGACCA 60.105 55.000 0.00 0.00 34.60 4.02
2047 2070 1.002544 GTTGGGGAGAAGACCACTGAG 59.997 57.143 0.00 0.00 36.27 3.35
2048 2071 0.545309 TGGGGAGAAGACCACTGAGG 60.545 60.000 0.00 0.00 45.67 3.86
2050 2073 1.599576 GGAGAAGACCACTGAGGCC 59.400 63.158 0.00 0.00 43.14 5.19
2054 2077 0.670854 GAAGACCACTGAGGCCGAAC 60.671 60.000 0.00 0.00 43.14 3.95
2068 2091 1.269051 GCCGAACCCAACAAGAAACAG 60.269 52.381 0.00 0.00 0.00 3.16
2077 2100 1.205064 CAAGAAACAGCGCACCTCG 59.795 57.895 11.47 0.00 42.12 4.63
2084 2107 0.884704 ACAGCGCACCTCGAACAATT 60.885 50.000 11.47 0.00 41.67 2.32
2290 2314 2.862541 TCATGTGGTCTCTGGGTTTTG 58.137 47.619 0.00 0.00 0.00 2.44
2315 2339 6.067263 TGGATGTTTTGTTGTTAGTAGTGC 57.933 37.500 0.00 0.00 0.00 4.40
2371 2395 2.141517 CCTCTGCAGAAGTGTCAGTTG 58.858 52.381 18.85 1.46 32.67 3.16
2402 2426 4.715520 ATAAGCGTTGTATTGATGCTCG 57.284 40.909 0.00 0.00 38.37 5.03
2421 2445 1.177401 GGGTGAAACTGAATGAGGGC 58.823 55.000 0.00 0.00 36.74 5.19
2426 2450 0.537143 AAACTGAATGAGGGCGTGCA 60.537 50.000 0.00 0.00 0.00 4.57
2455 2479 3.054287 TGCGACCTTTGTATATGGGGAAA 60.054 43.478 0.00 0.00 0.00 3.13
2470 2495 1.574702 GGAAACAAGGCGGGAAGACG 61.575 60.000 0.00 0.00 0.00 4.18
2473 2498 2.434359 CAAGGCGGGAAGACGGAC 60.434 66.667 0.00 0.00 0.00 4.79
2576 2604 3.242867 TCTCAGAGGATGAACACTTGGT 58.757 45.455 0.00 0.00 37.52 3.67
2596 2624 1.111277 TCATCGGGATCGCTCAAAGA 58.889 50.000 8.28 0.00 36.13 2.52
2654 2682 1.202879 TGGGTTAACTGACTTGGGCTG 60.203 52.381 5.42 0.00 0.00 4.85
2778 2806 6.183360 TGTTTGATAGTTGTGGTGTTGAGAAC 60.183 38.462 0.00 0.00 0.00 3.01
2823 2852 4.412199 CACTACCCCATCCTGATTTCCTTA 59.588 45.833 0.00 0.00 0.00 2.69
2825 2854 3.474920 ACCCCATCCTGATTTCCTTAGT 58.525 45.455 0.00 0.00 0.00 2.24
2832 2861 6.604795 CCATCCTGATTTCCTTAGTCAACAAT 59.395 38.462 0.00 0.00 0.00 2.71
2833 2862 7.415989 CCATCCTGATTTCCTTAGTCAACAATG 60.416 40.741 0.00 0.00 0.00 2.82
2834 2863 5.415701 TCCTGATTTCCTTAGTCAACAATGC 59.584 40.000 0.00 0.00 0.00 3.56
2835 2864 5.416952 CCTGATTTCCTTAGTCAACAATGCT 59.583 40.000 0.00 0.00 0.00 3.79
2836 2865 6.599244 CCTGATTTCCTTAGTCAACAATGCTA 59.401 38.462 0.00 0.00 0.00 3.49
2837 2866 7.121168 CCTGATTTCCTTAGTCAACAATGCTAA 59.879 37.037 0.00 0.00 0.00 3.09
2838 2867 8.579850 TGATTTCCTTAGTCAACAATGCTAAT 57.420 30.769 0.00 0.00 30.34 1.73
2839 2868 8.677300 TGATTTCCTTAGTCAACAATGCTAATC 58.323 33.333 0.00 0.00 30.34 1.75
2840 2869 8.814038 ATTTCCTTAGTCAACAATGCTAATCT 57.186 30.769 0.00 0.00 30.34 2.40
2841 2870 7.615582 TTCCTTAGTCAACAATGCTAATCTG 57.384 36.000 0.00 0.00 30.34 2.90
2842 2871 6.946340 TCCTTAGTCAACAATGCTAATCTGA 58.054 36.000 0.00 0.00 30.34 3.27
2843 2872 7.044181 TCCTTAGTCAACAATGCTAATCTGAG 58.956 38.462 0.00 0.00 30.34 3.35
2844 2873 6.820656 CCTTAGTCAACAATGCTAATCTGAGT 59.179 38.462 0.00 0.00 30.34 3.41
2845 2874 7.010923 CCTTAGTCAACAATGCTAATCTGAGTC 59.989 40.741 0.00 0.00 30.34 3.36
2846 2875 4.867047 AGTCAACAATGCTAATCTGAGTCG 59.133 41.667 0.00 0.00 0.00 4.18
2847 2876 4.627467 GTCAACAATGCTAATCTGAGTCGT 59.373 41.667 0.00 0.00 0.00 4.34
2848 2877 4.864806 TCAACAATGCTAATCTGAGTCGTC 59.135 41.667 0.00 0.00 0.00 4.20
2849 2878 3.786635 ACAATGCTAATCTGAGTCGTCC 58.213 45.455 0.00 0.00 0.00 4.79
2850 2879 3.449018 ACAATGCTAATCTGAGTCGTCCT 59.551 43.478 0.00 0.00 0.00 3.85
2851 2880 4.081420 ACAATGCTAATCTGAGTCGTCCTT 60.081 41.667 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 4.261656 CGGGTCCACAGTTATTAGCTAGAG 60.262 50.000 0.00 0.00 0.00 2.43
125 126 3.111484 TCTACATCAACACCATAGCCCA 58.889 45.455 0.00 0.00 0.00 5.36
188 192 2.090550 TGAGATCCCATCTTGGAGCCTA 60.091 50.000 0.00 0.00 41.84 3.93
354 369 1.457643 CCCACGAGATAGGAGGGCA 60.458 63.158 0.00 0.00 31.81 5.36
681 703 2.905415 TCATTGGCTGGAGGAAACAT 57.095 45.000 0.00 0.00 0.00 2.71
755 777 1.379527 CTATCTGGTCGGGTTTTGGC 58.620 55.000 0.00 0.00 0.00 4.52
769 791 2.220479 GGAACGCCGTTAAGCTATCT 57.780 50.000 0.79 0.00 0.00 1.98
1041 1063 6.202226 CGAGATCGTCTGAATGTGAAGATTA 58.798 40.000 0.00 0.00 33.97 1.75
1043 1065 4.605968 CGAGATCGTCTGAATGTGAAGAT 58.394 43.478 0.00 0.00 35.87 2.40
1044 1066 4.021191 CGAGATCGTCTGAATGTGAAGA 57.979 45.455 0.00 0.00 34.11 2.87
1080 1102 3.561120 TTTCGGATTGCCCCACGCT 62.561 57.895 0.00 0.00 38.78 5.07
1117 1139 3.683281 GCTACAAACACATTATCCCCCGA 60.683 47.826 0.00 0.00 0.00 5.14
1122 1144 6.907212 CGAATTCAGCTACAAACACATTATCC 59.093 38.462 6.22 0.00 0.00 2.59
1125 1147 5.703592 ACCGAATTCAGCTACAAACACATTA 59.296 36.000 6.22 0.00 0.00 1.90
1129 1151 4.142966 GGTACCGAATTCAGCTACAAACAC 60.143 45.833 6.22 0.00 0.00 3.32
1149 1171 0.639943 TGGACCTATCAGCCTGGGTA 59.360 55.000 0.00 0.00 28.82 3.69
1153 1175 0.692419 ACCCTGGACCTATCAGCCTG 60.692 60.000 0.00 0.00 0.00 4.85
1158 1180 1.216930 TCGATCACCCTGGACCTATCA 59.783 52.381 0.00 0.00 0.00 2.15
1161 1183 1.688311 CCTTCGATCACCCTGGACCTA 60.688 57.143 0.00 0.00 0.00 3.08
1164 1186 0.613777 AACCTTCGATCACCCTGGAC 59.386 55.000 0.00 0.00 0.00 4.02
1165 1187 0.902531 GAACCTTCGATCACCCTGGA 59.097 55.000 0.00 0.00 0.00 3.86
1174 1196 3.482156 CATCCATGGAGAACCTTCGAT 57.518 47.619 21.33 0.00 37.04 3.59
1200 1222 4.887071 ACCTTGAGAAGCACAACATGTTTA 59.113 37.500 8.77 0.00 30.84 2.01
1208 1230 3.351740 TCAAACACCTTGAGAAGCACAA 58.648 40.909 0.00 0.00 39.20 3.33
1209 1231 2.997980 TCAAACACCTTGAGAAGCACA 58.002 42.857 0.00 0.00 39.20 4.57
1218 1240 5.599732 TGAACATCCAAATCAAACACCTTG 58.400 37.500 0.00 0.00 36.25 3.61
1224 1246 6.089249 AGAGGTTGAACATCCAAATCAAAC 57.911 37.500 6.34 0.00 40.29 2.93
1231 1253 4.792068 ACTTGAAGAGGTTGAACATCCAA 58.208 39.130 6.34 4.21 27.29 3.53
1234 1256 6.861065 TTGTACTTGAAGAGGTTGAACATC 57.139 37.500 1.11 1.11 0.00 3.06
1239 1261 8.717821 CGATAAAATTGTACTTGAAGAGGTTGA 58.282 33.333 0.00 0.00 0.00 3.18
1251 1273 4.013728 TGGCCAAGCGATAAAATTGTACT 58.986 39.130 0.61 0.00 0.00 2.73
1254 1276 5.509501 CCATATGGCCAAGCGATAAAATTGT 60.510 40.000 10.96 0.00 33.40 2.71
1257 1279 3.511146 CCCATATGGCCAAGCGATAAAAT 59.489 43.478 16.97 0.00 33.40 1.82
1261 1283 3.955145 CCCATATGGCCAAGCGATA 57.045 52.632 16.97 0.00 34.12 2.92
1284 1306 1.862201 CTTGGCGGCAAATGCATAATG 59.138 47.619 25.45 6.64 44.36 1.90
1293 1315 2.192664 TCATAAGTCTTGGCGGCAAA 57.807 45.000 25.45 10.75 0.00 3.68
1299 1321 2.128771 TGGCCTTCATAAGTCTTGGC 57.871 50.000 3.32 2.88 39.61 4.52
1317 1339 2.417243 GGCGAATTCCATCCCAAGTTTG 60.417 50.000 0.00 0.00 0.00 2.93
1330 1352 1.681264 CCCTATGGGTTTGGCGAATTC 59.319 52.381 0.00 0.00 38.25 2.17
1338 1360 0.474184 AGATCCGCCCTATGGGTTTG 59.526 55.000 4.42 0.00 46.51 2.93
1344 1366 1.417890 ACTTTGGAGATCCGCCCTATG 59.582 52.381 0.15 0.00 39.43 2.23
1347 1369 1.604378 CACTTTGGAGATCCGCCCT 59.396 57.895 0.15 0.00 39.43 5.19
1362 1384 2.508716 ACCATCTGCATGAGATTCCACT 59.491 45.455 0.00 0.00 39.64 4.00
1368 1390 0.757512 AGCGACCATCTGCATGAGAT 59.242 50.000 0.00 0.00 42.70 2.75
1395 1417 4.821260 TCATCTCTCACTCTCATGTAGCTC 59.179 45.833 0.00 0.00 0.00 4.09
1396 1418 4.790937 TCATCTCTCACTCTCATGTAGCT 58.209 43.478 0.00 0.00 0.00 3.32
1398 1420 7.364970 CAATCTCATCTCTCACTCTCATGTAG 58.635 42.308 0.00 0.00 0.00 2.74
1400 1422 5.452216 GCAATCTCATCTCTCACTCTCATGT 60.452 44.000 0.00 0.00 0.00 3.21
1401 1423 4.986034 GCAATCTCATCTCTCACTCTCATG 59.014 45.833 0.00 0.00 0.00 3.07
1407 1429 4.222366 TGAACAGCAATCTCATCTCTCACT 59.778 41.667 0.00 0.00 0.00 3.41
1415 1437 3.438087 CGGTTCTTGAACAGCAATCTCAT 59.562 43.478 14.38 0.00 35.59 2.90
1434 1456 2.137523 GTCACATAACGAACAACCGGT 58.862 47.619 0.00 0.00 0.00 5.28
1438 1460 4.758561 GTGACTGTCACATAACGAACAAC 58.241 43.478 30.43 3.57 46.22 3.32
1463 1485 7.152645 AGTTTTCATAGTTCTGAGCTTTACGA 58.847 34.615 0.00 0.00 0.00 3.43
1464 1486 7.352719 AGTTTTCATAGTTCTGAGCTTTACG 57.647 36.000 0.00 0.00 0.00 3.18
1466 1488 9.998106 AGTAAGTTTTCATAGTTCTGAGCTTTA 57.002 29.630 0.00 0.00 0.00 1.85
1475 1497 9.209175 ACATCACTGAGTAAGTTTTCATAGTTC 57.791 33.333 0.00 0.00 36.83 3.01
1481 1503 8.988934 GTTCATACATCACTGAGTAAGTTTTCA 58.011 33.333 0.00 0.00 36.83 2.69
1482 1504 8.162880 CGTTCATACATCACTGAGTAAGTTTTC 58.837 37.037 0.00 0.00 36.83 2.29
1483 1505 7.117812 CCGTTCATACATCACTGAGTAAGTTTT 59.882 37.037 0.00 0.00 36.83 2.43
1494 1516 2.501723 AGGAAGCCGTTCATACATCACT 59.498 45.455 0.00 0.00 33.93 3.41
1506 1528 5.395435 GGAGAAATAGTAGAAAGGAAGCCGT 60.395 44.000 0.00 0.00 0.00 5.68
1512 1534 5.425539 CCCACAGGAGAAATAGTAGAAAGGA 59.574 44.000 0.00 0.00 33.47 3.36
1515 1537 4.783227 AGCCCACAGGAGAAATAGTAGAAA 59.217 41.667 0.00 0.00 33.47 2.52
1518 1540 3.070302 GGAGCCCACAGGAGAAATAGTAG 59.930 52.174 0.00 0.00 33.47 2.57
1519 1541 3.039011 GGAGCCCACAGGAGAAATAGTA 58.961 50.000 0.00 0.00 33.47 1.82
1523 1545 2.122768 CTAGGAGCCCACAGGAGAAAT 58.877 52.381 0.00 0.00 33.47 2.17
1524 1546 1.573108 CTAGGAGCCCACAGGAGAAA 58.427 55.000 0.00 0.00 33.47 2.52
1545 1567 4.656100 TGGACAAAGGATTGAGGAATGA 57.344 40.909 0.00 0.00 38.94 2.57
1548 1570 4.398319 GAGTTGGACAAAGGATTGAGGAA 58.602 43.478 0.00 0.00 38.94 3.36
1551 1573 2.744202 CGGAGTTGGACAAAGGATTGAG 59.256 50.000 0.00 0.00 38.94 3.02
1554 1576 1.271926 CCCGGAGTTGGACAAAGGATT 60.272 52.381 0.73 0.00 0.00 3.01
1558 1580 0.609131 ATGCCCGGAGTTGGACAAAG 60.609 55.000 0.73 0.00 0.00 2.77
1560 1582 1.002624 GATGCCCGGAGTTGGACAA 60.003 57.895 0.73 0.00 0.00 3.18
1563 1585 2.669133 CCTGATGCCCGGAGTTGGA 61.669 63.158 0.73 0.00 0.00 3.53
1566 1588 2.285368 TCCCTGATGCCCGGAGTT 60.285 61.111 0.73 0.00 0.00 3.01
1568 1590 4.227134 CGTCCCTGATGCCCGGAG 62.227 72.222 0.73 0.00 0.00 4.63
1576 1598 0.031111 TCCCCATTCTCGTCCCTGAT 60.031 55.000 0.00 0.00 0.00 2.90
1581 1603 1.522569 CAGGTCCCCATTCTCGTCC 59.477 63.158 0.00 0.00 0.00 4.79
1584 1606 1.915078 AAGGCAGGTCCCCATTCTCG 61.915 60.000 0.00 0.00 34.51 4.04
1587 1609 1.986882 CATAAGGCAGGTCCCCATTC 58.013 55.000 0.00 0.00 34.51 2.67
1599 1621 3.248266 CAACTTCTTTGCAGCATAAGGC 58.752 45.455 14.08 0.00 45.30 4.35
1617 1639 1.503818 AATCACCGGTCACACGCAAC 61.504 55.000 2.59 0.00 0.00 4.17
1621 1643 1.724623 CAAGTAATCACCGGTCACACG 59.275 52.381 2.59 0.00 0.00 4.49
1629 1651 4.177026 CTGACTTCCTCAAGTAATCACCG 58.823 47.826 0.00 0.00 43.37 4.94
1631 1653 4.932200 CACCTGACTTCCTCAAGTAATCAC 59.068 45.833 0.00 0.00 43.37 3.06
1634 1656 4.168101 TCCACCTGACTTCCTCAAGTAAT 58.832 43.478 0.00 0.00 43.37 1.89
1635 1657 3.583228 TCCACCTGACTTCCTCAAGTAA 58.417 45.455 0.00 0.00 43.37 2.24
1636 1658 3.254093 TCCACCTGACTTCCTCAAGTA 57.746 47.619 0.00 0.00 43.37 2.24
1638 1660 2.417924 CGATCCACCTGACTTCCTCAAG 60.418 54.545 0.00 0.00 35.50 3.02
1639 1661 1.550524 CGATCCACCTGACTTCCTCAA 59.449 52.381 0.00 0.00 0.00 3.02
1640 1662 1.186200 CGATCCACCTGACTTCCTCA 58.814 55.000 0.00 0.00 0.00 3.86
1647 1669 2.223618 GCTAGACTTCGATCCACCTGAC 60.224 54.545 0.00 0.00 0.00 3.51
1650 1672 2.145397 TGCTAGACTTCGATCCACCT 57.855 50.000 0.00 0.00 0.00 4.00
1653 1675 2.168313 TGCATTGCTAGACTTCGATCCA 59.832 45.455 10.49 0.00 0.00 3.41
1656 1678 4.063998 TGATGCATTGCTAGACTTCGAT 57.936 40.909 10.49 0.00 0.00 3.59
1659 1681 5.389620 CGATGATGATGCATTGCTAGACTTC 60.390 44.000 10.49 6.94 0.00 3.01
1665 1687 1.808343 GCCGATGATGATGCATTGCTA 59.192 47.619 10.49 0.00 0.00 3.49
1668 1690 1.666023 GCTGCCGATGATGATGCATTG 60.666 52.381 0.00 0.00 32.53 2.82
1678 1700 1.953231 CTCTCACCAGCTGCCGATGA 61.953 60.000 8.66 8.01 0.00 2.92
1680 1702 0.684479 TACTCTCACCAGCTGCCGAT 60.684 55.000 8.66 0.00 0.00 4.18
1683 1705 0.321671 TGTTACTCTCACCAGCTGCC 59.678 55.000 8.66 0.00 0.00 4.85
1686 1708 4.772624 TCAGTATTGTTACTCTCACCAGCT 59.227 41.667 0.00 0.00 36.50 4.24
1688 1710 5.521735 GCATCAGTATTGTTACTCTCACCAG 59.478 44.000 0.00 0.00 36.50 4.00
1692 1714 5.125578 ACGAGCATCAGTATTGTTACTCTCA 59.874 40.000 0.00 0.00 36.50 3.27
1696 1718 4.864806 CACACGAGCATCAGTATTGTTACT 59.135 41.667 0.00 0.00 39.30 2.24
1697 1719 4.492570 GCACACGAGCATCAGTATTGTTAC 60.493 45.833 0.00 0.00 33.17 2.50
1698 1720 3.616821 GCACACGAGCATCAGTATTGTTA 59.383 43.478 0.00 0.00 33.17 2.41
1702 1724 1.208052 AGGCACACGAGCATCAGTATT 59.792 47.619 0.00 0.00 35.83 1.89
1706 1728 0.390866 AGAAGGCACACGAGCATCAG 60.391 55.000 0.00 0.00 35.83 2.90
1709 1731 0.035317 TGAAGAAGGCACACGAGCAT 59.965 50.000 0.00 0.00 35.83 3.79
1725 1747 2.282180 GCCTTTGGTCGGCCTGAA 60.282 61.111 7.97 0.86 41.73 3.02
1730 1752 0.878523 GTTTTTGGCCTTTGGTCGGC 60.879 55.000 3.32 0.00 46.83 5.54
1734 1756 1.065782 GTGTGGTTTTTGGCCTTTGGT 60.066 47.619 3.32 0.00 0.00 3.67
1735 1757 1.065854 TGTGTGGTTTTTGGCCTTTGG 60.066 47.619 3.32 0.00 0.00 3.28
1737 1759 1.209261 CCTGTGTGGTTTTTGGCCTTT 59.791 47.619 3.32 0.00 0.00 3.11
1752 1774 1.016130 CGCCACTAGCAGAACCTGTG 61.016 60.000 0.00 0.00 44.04 3.66
1758 1780 2.571757 CCGTCGCCACTAGCAGAA 59.428 61.111 0.00 0.00 44.04 3.02
1763 1785 3.528370 CCTCCCCGTCGCCACTAG 61.528 72.222 0.00 0.00 0.00 2.57
1770 1792 4.530857 GATGGCACCTCCCCGTCG 62.531 72.222 0.00 0.00 0.00 5.12
1773 1795 3.866582 GGAGATGGCACCTCCCCG 61.867 72.222 17.90 0.00 43.37 5.73
1808 1830 1.002087 ACCACGTCCATGAGAAGAACC 59.998 52.381 0.00 0.00 0.00 3.62
1810 1832 1.067846 CGACCACGTCCATGAGAAGAA 60.068 52.381 0.00 0.00 34.56 2.52
1811 1833 0.526211 CGACCACGTCCATGAGAAGA 59.474 55.000 0.00 0.00 34.56 2.87
1812 1834 0.458543 CCGACCACGTCCATGAGAAG 60.459 60.000 0.00 0.00 37.88 2.85
1813 1835 1.589630 CCGACCACGTCCATGAGAA 59.410 57.895 0.00 0.00 37.88 2.87
1814 1836 3.001902 GCCGACCACGTCCATGAGA 62.002 63.158 0.00 0.00 37.88 3.27
1816 1838 4.077184 GGCCGACCACGTCCATGA 62.077 66.667 0.00 0.00 37.50 3.07
1818 1840 4.082523 CAGGCCGACCACGTCCAT 62.083 66.667 0.00 0.00 40.20 3.41
1835 1857 4.397832 TTTACCACGGCCCCGAGC 62.398 66.667 14.44 0.00 42.83 5.03
1843 1865 4.789123 CCCCGCCCTTTACCACGG 62.789 72.222 0.00 0.00 45.21 4.94
1846 1868 4.354162 GCACCCCGCCCTTTACCA 62.354 66.667 0.00 0.00 32.94 3.25
1849 1871 2.265467 GATCAGCACCCCGCCCTTTA 62.265 60.000 0.00 0.00 44.04 1.85
1858 1880 1.742768 CCTACTCGGATCAGCACCC 59.257 63.158 0.00 0.00 33.16 4.61
1860 1882 0.671251 CTCCCTACTCGGATCAGCAC 59.329 60.000 0.00 0.00 33.16 4.40
1863 1885 2.379972 ACAACTCCCTACTCGGATCAG 58.620 52.381 0.00 0.00 33.16 2.90
1866 1888 3.195825 CAGAAACAACTCCCTACTCGGAT 59.804 47.826 0.00 0.00 33.16 4.18
1867 1889 2.561419 CAGAAACAACTCCCTACTCGGA 59.439 50.000 0.00 0.00 33.16 4.55
1868 1890 2.353803 CCAGAAACAACTCCCTACTCGG 60.354 54.545 0.00 0.00 0.00 4.63
1870 1892 4.282703 TGTACCAGAAACAACTCCCTACTC 59.717 45.833 0.00 0.00 0.00 2.59
1871 1893 4.228824 TGTACCAGAAACAACTCCCTACT 58.771 43.478 0.00 0.00 0.00 2.57
1885 1907 4.776349 TGCTCTTCTTTTGTTGTACCAGA 58.224 39.130 0.00 0.00 0.00 3.86
1888 1910 5.333111 CGTACTGCTCTTCTTTTGTTGTACC 60.333 44.000 0.00 0.00 0.00 3.34
1891 1913 4.270325 GTCGTACTGCTCTTCTTTTGTTGT 59.730 41.667 0.00 0.00 0.00 3.32
1905 1928 0.456312 CTTCTGACCGGTCGTACTGC 60.456 60.000 28.70 5.10 0.00 4.40
1906 1929 1.130749 CTCTTCTGACCGGTCGTACTG 59.869 57.143 28.70 17.09 0.00 2.74
1915 1938 3.077359 AGCAAATTTCCTCTTCTGACCG 58.923 45.455 0.00 0.00 0.00 4.79
1918 1941 5.940470 GTCCTTAGCAAATTTCCTCTTCTGA 59.060 40.000 0.00 0.00 0.00 3.27
1932 1955 1.419762 TCACAGCTTGGTCCTTAGCAA 59.580 47.619 15.93 0.00 40.68 3.91
1939 1962 1.896220 TCAATGTCACAGCTTGGTCC 58.104 50.000 0.00 0.00 0.00 4.46
1941 1964 4.022589 CAGAATTCAATGTCACAGCTTGGT 60.023 41.667 8.44 0.00 0.00 3.67
1949 1972 5.245531 TGTACTCCCAGAATTCAATGTCAC 58.754 41.667 8.44 0.00 0.00 3.67
1950 1973 5.497464 TGTACTCCCAGAATTCAATGTCA 57.503 39.130 8.44 0.00 0.00 3.58
1954 1977 4.478317 TCCCATGTACTCCCAGAATTCAAT 59.522 41.667 8.44 0.00 0.00 2.57
1955 1978 3.849574 TCCCATGTACTCCCAGAATTCAA 59.150 43.478 8.44 0.00 0.00 2.69
1956 1979 3.455910 CTCCCATGTACTCCCAGAATTCA 59.544 47.826 8.44 0.00 0.00 2.57
1959 1982 3.421394 TCTCCCATGTACTCCCAGAAT 57.579 47.619 0.00 0.00 0.00 2.40
1960 1983 2.940514 TCTCCCATGTACTCCCAGAA 57.059 50.000 0.00 0.00 0.00 3.02
1961 1984 2.940514 TTCTCCCATGTACTCCCAGA 57.059 50.000 0.00 0.00 0.00 3.86
1962 1985 2.486191 GCATTCTCCCATGTACTCCCAG 60.486 54.545 0.00 0.00 0.00 4.45
1966 1989 3.629398 CCAAAGCATTCTCCCATGTACTC 59.371 47.826 0.00 0.00 0.00 2.59
1967 1990 3.624777 CCAAAGCATTCTCCCATGTACT 58.375 45.455 0.00 0.00 0.00 2.73
1968 1991 2.099756 GCCAAAGCATTCTCCCATGTAC 59.900 50.000 0.00 0.00 39.53 2.90
1970 1993 1.188863 GCCAAAGCATTCTCCCATGT 58.811 50.000 0.00 0.00 39.53 3.21
1971 1994 1.407979 GAGCCAAAGCATTCTCCCATG 59.592 52.381 0.00 0.00 43.56 3.66
1973 1996 0.700564 AGAGCCAAAGCATTCTCCCA 59.299 50.000 0.00 0.00 43.56 4.37
1974 1997 1.475682 CAAGAGCCAAAGCATTCTCCC 59.524 52.381 0.00 0.00 43.56 4.30
1976 1999 3.366781 GGAACAAGAGCCAAAGCATTCTC 60.367 47.826 0.00 0.00 43.56 2.87
1977 2000 2.560105 GGAACAAGAGCCAAAGCATTCT 59.440 45.455 0.00 0.00 43.56 2.40
1978 2001 2.353109 GGGAACAAGAGCCAAAGCATTC 60.353 50.000 0.00 0.00 43.56 2.67
1985 2008 1.270839 CGAAGAGGGAACAAGAGCCAA 60.271 52.381 0.00 0.00 0.00 4.52
1987 2010 0.608640 TCGAAGAGGGAACAAGAGCC 59.391 55.000 0.00 0.00 0.00 4.70
2005 2028 2.098614 TCAGAGACATCAGGAGCACTC 58.901 52.381 0.00 0.00 0.00 3.51
2006 2029 2.101783 CTCAGAGACATCAGGAGCACT 58.898 52.381 0.00 0.00 0.00 4.40
2008 2031 1.272928 ACCTCAGAGACATCAGGAGCA 60.273 52.381 0.00 0.00 31.36 4.26
2010 2033 2.168106 CCAACCTCAGAGACATCAGGAG 59.832 54.545 0.00 0.00 0.00 3.69
2016 2039 1.079490 TCTCCCCAACCTCAGAGACAT 59.921 52.381 0.00 0.00 30.56 3.06
2017 2040 0.487325 TCTCCCCAACCTCAGAGACA 59.513 55.000 0.00 0.00 30.56 3.41
2019 2042 1.433199 TCTTCTCCCCAACCTCAGAGA 59.567 52.381 0.00 0.00 33.65 3.10
2022 2045 0.615850 GGTCTTCTCCCCAACCTCAG 59.384 60.000 0.00 0.00 0.00 3.35
2023 2046 0.104672 TGGTCTTCTCCCCAACCTCA 60.105 55.000 0.00 0.00 32.82 3.86
2024 2047 0.325272 GTGGTCTTCTCCCCAACCTC 59.675 60.000 0.00 0.00 32.82 3.85
2025 2048 0.104409 AGTGGTCTTCTCCCCAACCT 60.104 55.000 0.00 0.00 32.82 3.50
2026 2049 0.036875 CAGTGGTCTTCTCCCCAACC 59.963 60.000 0.00 0.00 31.17 3.77
2028 2051 1.352083 CTCAGTGGTCTTCTCCCCAA 58.648 55.000 0.00 0.00 31.17 4.12
2029 2052 0.545309 CCTCAGTGGTCTTCTCCCCA 60.545 60.000 0.00 0.00 0.00 4.96
2039 2062 3.637273 GGGTTCGGCCTCAGTGGT 61.637 66.667 0.00 0.00 38.35 4.16
2040 2063 3.190738 TTGGGTTCGGCCTCAGTGG 62.191 63.158 0.00 0.00 37.43 4.00
2042 2065 1.990160 TTGTTGGGTTCGGCCTCAGT 61.990 55.000 0.00 0.00 37.43 3.41
2047 2070 0.031585 GTTTCTTGTTGGGTTCGGCC 59.968 55.000 0.00 0.00 0.00 6.13
2048 2071 0.741915 TGTTTCTTGTTGGGTTCGGC 59.258 50.000 0.00 0.00 0.00 5.54
2050 2073 1.596954 CGCTGTTTCTTGTTGGGTTCG 60.597 52.381 0.00 0.00 0.00 3.95
2054 2077 0.594796 GTGCGCTGTTTCTTGTTGGG 60.595 55.000 9.73 0.00 0.00 4.12
2068 2091 0.447801 ATCAATTGTTCGAGGTGCGC 59.552 50.000 0.00 0.00 40.61 6.09
2077 2100 1.264288 GGATCCGCCGATCAATTGTTC 59.736 52.381 15.51 5.88 45.89 3.18
2106 2129 1.344953 TTGGCGGGGATGCTCTACAT 61.345 55.000 0.00 0.00 43.54 2.29
2109 2132 1.223487 GTTTGGCGGGGATGCTCTA 59.777 57.895 0.00 0.00 34.52 2.43
2290 2314 6.142817 CACTACTAACAACAAAACATCCAGC 58.857 40.000 0.00 0.00 0.00 4.85
2315 2339 0.673644 CAAGCCACCACTAAGACCCG 60.674 60.000 0.00 0.00 0.00 5.28
2371 2395 1.664151 ACAACGCTTATTAGCCGCTTC 59.336 47.619 0.00 0.00 44.86 3.86
2402 2426 1.177401 GCCCTCATTCAGTTTCACCC 58.823 55.000 0.00 0.00 0.00 4.61
2426 2450 2.372040 TACAAAGGTCGCACGCCAGT 62.372 55.000 6.35 4.72 0.00 4.00
2455 2479 2.920912 TCCGTCTTCCCGCCTTGT 60.921 61.111 0.00 0.00 0.00 3.16
2470 2495 0.907230 AGCTCCCAGAACTGAGGTCC 60.907 60.000 0.00 0.00 34.40 4.46
2473 2498 1.274712 AGAAGCTCCCAGAACTGAGG 58.725 55.000 3.19 3.63 0.00 3.86
2573 2601 1.326951 TGAGCGATCCCGATGAACCA 61.327 55.000 0.00 0.00 38.22 3.67
2574 2602 0.179084 TTGAGCGATCCCGATGAACC 60.179 55.000 0.00 0.00 38.22 3.62
2576 2604 1.480545 TCTTTGAGCGATCCCGATGAA 59.519 47.619 0.00 0.00 38.22 2.57
2579 2607 1.067821 GAGTCTTTGAGCGATCCCGAT 59.932 52.381 0.00 0.00 38.22 4.18
2596 2624 6.558488 ATCTCTAAAGGCTGAAATCTGAGT 57.442 37.500 0.00 0.00 0.00 3.41
2654 2682 4.709886 ACCATGTAAATTTAGGACCCAAGC 59.290 41.667 8.55 0.00 0.00 4.01
2692 2720 2.493278 GGCACTTGACATGGCTATTTGT 59.507 45.455 0.00 0.00 39.45 2.83
2778 2806 5.525378 GTGATCTTAAGTAGTGGCAATGAGG 59.475 44.000 1.63 0.00 0.00 3.86
2823 2852 4.867047 CGACTCAGATTAGCATTGTTGACT 59.133 41.667 0.00 0.00 0.00 3.41
2825 2854 4.820897 ACGACTCAGATTAGCATTGTTGA 58.179 39.130 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.