Multiple sequence alignment - TraesCS3B01G508800

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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 TraesCS3B01G508800 chr3B 100.000 3792 0 0 1 3792 752912809 752916600 0.000000e+00 7003.0
1 TraesCS3B01G508800 chr3B 93.282 521 32 2 22 541 348523289 348522771 0.000000e+00 765.0
2 TraesCS3B01G508800 chr3B 83.788 586 82 10 1969 2550 752173991 752174567 9.260000e-151 544.0
3 TraesCS3B01G508800 chr3B 79.181 586 110 10 2205 2783 408345508 408344928 2.750000e-106 396.0
4 TraesCS3B01G508800 chr3D 96.094 1869 60 8 1708 3566 565145682 565143817 0.000000e+00 3035.0
5 TraesCS3B01G508800 chr3D 96.608 737 24 1 539 1274 565146836 565146100 0.000000e+00 1221.0
6 TraesCS3B01G508800 chr3D 78.994 1014 136 31 1968 2953 564393849 564394813 4.160000e-174 621.0
7 TraesCS3B01G508800 chr3D 83.439 471 71 5 1968 2436 564493426 564493891 7.530000e-117 431.0
8 TraesCS3B01G508800 chr3D 98.729 236 2 1 1473 1708 565146115 565145881 5.860000e-113 418.0
9 TraesCS3B01G508800 chr3D 94.000 150 8 1 3643 3792 565119686 565119538 3.810000e-55 226.0
10 TraesCS3B01G508800 chr3D 98.077 52 1 0 3594 3645 565143723 565143672 1.450000e-14 91.6
11 TraesCS3B01G508800 chr3A 96.729 1284 41 1 1708 2990 699547024 699545741 0.000000e+00 2137.0
12 TraesCS3B01G508800 chr3A 94.980 737 29 5 539 1274 699548175 699547446 0.000000e+00 1149.0
13 TraesCS3B01G508800 chr3A 92.683 533 33 3 2983 3511 699545552 699545022 0.000000e+00 763.0
14 TraesCS3B01G508800 chr3A 81.456 879 143 11 2214 3090 699105262 699106122 0.000000e+00 702.0
15 TraesCS3B01G508800 chr3A 97.034 236 7 0 1473 1708 699547461 699547226 7.630000e-107 398.0
16 TraesCS3B01G508800 chr3A 81.381 478 61 12 1958 2434 699229278 699229728 7.740000e-97 364.0
17 TraesCS3B01G508800 chr3A 96.429 196 6 1 1259 1454 221275762 221275568 4.730000e-84 322.0
18 TraesCS3B01G508800 chr3A 96.875 192 5 1 1263 1454 534547553 534547743 1.700000e-83 320.0
19 TraesCS3B01G508800 chr3A 90.594 202 15 3 3591 3791 699545025 699544827 8.080000e-67 265.0
20 TraesCS3B01G508800 chr3A 75.063 397 74 13 2393 2783 584112192 584111815 1.090000e-35 161.0
21 TraesCS3B01G508800 chr1B 93.905 525 28 2 22 545 181862413 181861892 0.000000e+00 789.0
22 TraesCS3B01G508800 chr1B 92.678 519 33 3 22 538 602416689 602416174 0.000000e+00 743.0
23 TraesCS3B01G508800 chr7D 93.295 522 32 3 21 541 285144214 285144733 0.000000e+00 767.0
24 TraesCS3B01G508800 chr7D 80.513 585 96 15 2205 2779 89290031 89290607 2.090000e-117 433.0
25 TraesCS3B01G508800 chr7D 77.670 103 15 7 1080 1178 546753316 546753414 5.290000e-04 56.5
26 TraesCS3B01G508800 chr5B 93.243 518 32 2 22 538 522364177 522363662 0.000000e+00 760.0
27 TraesCS3B01G508800 chr5B 93.243 518 31 3 22 538 578684834 578684320 0.000000e+00 760.0
28 TraesCS3B01G508800 chr5B 79.970 659 116 13 2130 2779 248389154 248388503 4.430000e-129 472.0
29 TraesCS3B01G508800 chr5B 74.532 267 62 6 991 1254 24146490 24146227 1.110000e-20 111.0
30 TraesCS3B01G508800 chr6B 93.077 520 32 2 22 540 69918079 69918595 0.000000e+00 758.0
31 TraesCS3B01G508800 chr6B 93.064 519 32 2 22 539 286361279 286360764 0.000000e+00 756.0
32 TraesCS3B01G508800 chr6B 94.419 215 9 2 1253 1464 1159908 1160122 1.020000e-85 327.0
33 TraesCS3B01G508800 chr6B 75.768 586 117 22 2212 2783 700251079 700251653 4.830000e-69 272.0
34 TraesCS3B01G508800 chr2B 93.090 521 31 3 19 538 615299682 615300198 0.000000e+00 758.0
35 TraesCS3B01G508800 chr2B 96.875 192 5 1 1264 1454 64626800 64626609 1.700000e-83 320.0
36 TraesCS3B01G508800 chr2B 96.875 192 5 1 1264 1454 71234638 71234447 1.700000e-83 320.0
37 TraesCS3B01G508800 chr7A 80.069 582 100 14 2205 2778 90477605 90478178 5.860000e-113 418.0
38 TraesCS3B01G508800 chr7A 78.481 158 24 9 1072 1224 630034602 630034754 1.120000e-15 95.3
39 TraesCS3B01G508800 chr7B 79.795 584 101 15 2205 2779 40194776 40195351 3.530000e-110 409.0
40 TraesCS3B01G508800 chr7B 97.354 189 5 0 1271 1459 440006182 440005994 4.730000e-84 322.0
41 TraesCS3B01G508800 chr6D 79.275 579 101 16 2212 2779 155840531 155839961 1.650000e-103 387.0
42 TraesCS3B01G508800 chr2A 97.895 190 3 1 1266 1455 568281108 568280920 1.020000e-85 327.0
43 TraesCS3B01G508800 chr1A 96.040 202 6 2 1254 1455 230139657 230139856 1.020000e-85 327.0
44 TraesCS3B01G508800 chr5A 77.397 584 108 19 2211 2779 42282029 42281455 3.650000e-85 326.0
45 TraesCS3B01G508800 chr5A 96.875 192 5 1 1263 1454 694976134 694975944 1.700000e-83 320.0
46 TraesCS3B01G508800 chr5A 79.478 268 47 7 2790 3056 297721372 297721112 2.330000e-42 183.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G508800 chr3B 752912809 752916600 3791 False 7003.0 7003 100.000 1 3792 1 chr3B.!!$F2 3791
1 TraesCS3B01G508800 chr3B 348522771 348523289 518 True 765.0 765 93.282 22 541 1 chr3B.!!$R1 519
2 TraesCS3B01G508800 chr3B 752173991 752174567 576 False 544.0 544 83.788 1969 2550 1 chr3B.!!$F1 581
3 TraesCS3B01G508800 chr3B 408344928 408345508 580 True 396.0 396 79.181 2205 2783 1 chr3B.!!$R2 578
4 TraesCS3B01G508800 chr3D 565143672 565146836 3164 True 1191.4 3035 97.377 539 3645 4 chr3D.!!$R2 3106
5 TraesCS3B01G508800 chr3D 564393849 564394813 964 False 621.0 621 78.994 1968 2953 1 chr3D.!!$F1 985
6 TraesCS3B01G508800 chr3A 699544827 699548175 3348 True 942.4 2137 94.404 539 3791 5 chr3A.!!$R3 3252
7 TraesCS3B01G508800 chr3A 699105262 699106122 860 False 702.0 702 81.456 2214 3090 1 chr3A.!!$F2 876
8 TraesCS3B01G508800 chr1B 181861892 181862413 521 True 789.0 789 93.905 22 545 1 chr1B.!!$R1 523
9 TraesCS3B01G508800 chr1B 602416174 602416689 515 True 743.0 743 92.678 22 538 1 chr1B.!!$R2 516
10 TraesCS3B01G508800 chr7D 285144214 285144733 519 False 767.0 767 93.295 21 541 1 chr7D.!!$F2 520
11 TraesCS3B01G508800 chr7D 89290031 89290607 576 False 433.0 433 80.513 2205 2779 1 chr7D.!!$F1 574
12 TraesCS3B01G508800 chr5B 522363662 522364177 515 True 760.0 760 93.243 22 538 1 chr5B.!!$R3 516
13 TraesCS3B01G508800 chr5B 578684320 578684834 514 True 760.0 760 93.243 22 538 1 chr5B.!!$R4 516
14 TraesCS3B01G508800 chr5B 248388503 248389154 651 True 472.0 472 79.970 2130 2779 1 chr5B.!!$R2 649
15 TraesCS3B01G508800 chr6B 69918079 69918595 516 False 758.0 758 93.077 22 540 1 chr6B.!!$F2 518
16 TraesCS3B01G508800 chr6B 286360764 286361279 515 True 756.0 756 93.064 22 539 1 chr6B.!!$R1 517
17 TraesCS3B01G508800 chr6B 700251079 700251653 574 False 272.0 272 75.768 2212 2783 1 chr6B.!!$F3 571
18 TraesCS3B01G508800 chr2B 615299682 615300198 516 False 758.0 758 93.090 19 538 1 chr2B.!!$F1 519
19 TraesCS3B01G508800 chr7A 90477605 90478178 573 False 418.0 418 80.069 2205 2778 1 chr7A.!!$F1 573
20 TraesCS3B01G508800 chr7B 40194776 40195351 575 False 409.0 409 79.795 2205 2779 1 chr7B.!!$F1 574
21 TraesCS3B01G508800 chr6D 155839961 155840531 570 True 387.0 387 79.275 2212 2779 1 chr6D.!!$R1 567
22 TraesCS3B01G508800 chr5A 42281455 42282029 574 True 326.0 326 77.397 2211 2779 1 chr5A.!!$R1 568

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
369 371 5.242615 TGCTTAGCTGATCTCTTGTATCGAT 59.757 40.0 5.60 2.16 0.00 3.59 F
1296 1300 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.0 14.15 0.00 44.29 3.32 F
1332 1336 0.036875 CCAGGAAAGGGTCTGACCAC 59.963 60.0 26.94 16.44 41.02 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1313 1317 0.036875 GTGGTCAGACCCTTTCCTGG 59.963 60.000 17.59 0.0 37.50 4.45 R
2757 3006 1.417890 ACCAAGTCACCTTCACTGAGG 59.582 52.381 0.00 0.0 42.75 3.86 R
2856 3106 2.762327 AGAGCCCTTTTCGTCGGTATTA 59.238 45.455 0.00 0.0 0.00 0.98 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
197 198 8.066668 CTTGTTAAGCTCGTTAAGGATATGAG 57.933 38.462 0.00 0.00 30.93 2.90
258 259 9.295214 TGTTTGTGAACATTGTACATGTTTAAG 57.705 29.630 18.45 0.00 41.76 1.85
369 371 5.242615 TGCTTAGCTGATCTCTTGTATCGAT 59.757 40.000 5.60 2.16 0.00 3.59
567 570 7.294958 AGAATGCCTATTACCAGGGTAATAAGT 59.705 37.037 23.96 13.62 46.46 2.24
579 582 8.165397 ACCAGGGTAATAAGTGCTAAGTTTTTA 58.835 33.333 0.00 0.00 0.00 1.52
679 682 6.697892 GTGTCTAGTGTCTATGCTAATGGTTC 59.302 42.308 0.00 0.00 0.00 3.62
1025 1029 2.821378 CACAACTGGAGCCAATGATGAA 59.179 45.455 8.47 0.00 0.00 2.57
1087 1091 5.163903 TGTTGTGTGCATTATACTAGTTGCG 60.164 40.000 11.58 0.00 37.92 4.85
1093 1097 5.462068 GTGCATTATACTAGTTGCGTGATGA 59.538 40.000 11.58 0.00 37.92 2.92
1236 1240 2.688507 GATGATCCCATCGTTATGCGT 58.311 47.619 0.00 0.00 39.70 5.24
1237 1241 2.613026 TGATCCCATCGTTATGCGTT 57.387 45.000 0.00 0.00 42.13 4.84
1265 1269 6.788243 TGCATATCTTTACTTGCACAGATTG 58.212 36.000 0.00 0.00 39.98 2.67
1266 1270 6.375174 TGCATATCTTTACTTGCACAGATTGT 59.625 34.615 0.00 0.00 39.98 2.71
1267 1271 7.094248 TGCATATCTTTACTTGCACAGATTGTT 60.094 33.333 0.00 0.00 39.98 2.83
1268 1272 7.756722 GCATATCTTTACTTGCACAGATTGTTT 59.243 33.333 0.00 0.00 35.22 2.83
1269 1273 9.282247 CATATCTTTACTTGCACAGATTGTTTC 57.718 33.333 0.00 0.00 0.00 2.78
1270 1274 6.691754 TCTTTACTTGCACAGATTGTTTCA 57.308 33.333 0.00 0.00 0.00 2.69
1271 1275 7.094508 TCTTTACTTGCACAGATTGTTTCAA 57.905 32.000 0.00 0.00 0.00 2.69
1272 1276 7.542890 TCTTTACTTGCACAGATTGTTTCAAA 58.457 30.769 0.00 0.00 0.00 2.69
1273 1277 8.196771 TCTTTACTTGCACAGATTGTTTCAAAT 58.803 29.630 0.00 0.00 0.00 2.32
1274 1278 7.697352 TTACTTGCACAGATTGTTTCAAATG 57.303 32.000 0.00 0.00 0.00 2.32
1275 1279 5.051816 ACTTGCACAGATTGTTTCAAATGG 58.948 37.500 0.00 0.00 0.00 3.16
1276 1280 3.992643 TGCACAGATTGTTTCAAATGGG 58.007 40.909 0.00 0.00 0.00 4.00
1277 1281 3.244146 TGCACAGATTGTTTCAAATGGGG 60.244 43.478 0.00 0.00 0.00 4.96
1278 1282 3.328505 CACAGATTGTTTCAAATGGGGC 58.671 45.455 0.00 0.00 0.00 5.80
1279 1283 2.971330 ACAGATTGTTTCAAATGGGGCA 59.029 40.909 0.00 0.00 0.00 5.36
1280 1284 3.390639 ACAGATTGTTTCAAATGGGGCAA 59.609 39.130 0.00 0.00 0.00 4.52
1281 1285 3.747529 CAGATTGTTTCAAATGGGGCAAC 59.252 43.478 0.00 0.00 0.00 4.17
1293 1297 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
1294 1298 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
1295 1299 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
1296 1300 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
1297 1301 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
1303 1307 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
1304 1308 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
1305 1309 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
1306 1310 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
1309 1313 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
1318 1322 4.020617 CTTGCGCAGGGTCCAGGA 62.021 66.667 12.39 0.00 0.00 3.86
1319 1323 3.551496 CTTGCGCAGGGTCCAGGAA 62.551 63.158 12.39 0.00 0.00 3.36
1320 1324 3.126703 TTGCGCAGGGTCCAGGAAA 62.127 57.895 11.31 0.00 0.00 3.13
1321 1325 2.747855 GCGCAGGGTCCAGGAAAG 60.748 66.667 0.30 0.00 0.00 2.62
1322 1326 2.045926 CGCAGGGTCCAGGAAAGG 60.046 66.667 0.00 0.00 0.00 3.11
1323 1327 2.356667 GCAGGGTCCAGGAAAGGG 59.643 66.667 0.00 0.00 0.00 3.95
1324 1328 2.539081 GCAGGGTCCAGGAAAGGGT 61.539 63.158 0.00 0.00 0.00 4.34
1325 1329 1.685820 CAGGGTCCAGGAAAGGGTC 59.314 63.158 0.00 0.00 0.00 4.46
1326 1330 0.842467 CAGGGTCCAGGAAAGGGTCT 60.842 60.000 0.00 0.00 0.00 3.85
1327 1331 0.842467 AGGGTCCAGGAAAGGGTCTG 60.842 60.000 0.00 0.00 0.00 3.51
1328 1332 0.840722 GGGTCCAGGAAAGGGTCTGA 60.841 60.000 0.00 0.00 33.11 3.27
1329 1333 0.325272 GGTCCAGGAAAGGGTCTGAC 59.675 60.000 0.00 0.00 33.11 3.51
1330 1334 0.325272 GTCCAGGAAAGGGTCTGACC 59.675 60.000 18.65 18.65 37.60 4.02
1331 1335 0.104672 TCCAGGAAAGGGTCTGACCA 60.105 55.000 26.94 1.36 41.02 4.02
1332 1336 0.036875 CCAGGAAAGGGTCTGACCAC 59.963 60.000 26.94 16.44 41.02 4.16
1333 1337 1.059913 CAGGAAAGGGTCTGACCACT 58.940 55.000 26.94 18.28 41.02 4.00
1334 1338 1.421646 CAGGAAAGGGTCTGACCACTT 59.578 52.381 26.94 22.33 41.02 3.16
1335 1339 2.136026 AGGAAAGGGTCTGACCACTTT 58.864 47.619 28.19 28.19 41.02 2.66
1336 1340 2.158608 AGGAAAGGGTCTGACCACTTTG 60.159 50.000 30.73 0.00 41.02 2.77
1337 1341 2.230660 GAAAGGGTCTGACCACTTTGG 58.769 52.381 30.73 0.00 41.02 3.28
1338 1342 0.478507 AAGGGTCTGACCACTTTGGG 59.521 55.000 26.94 0.00 43.37 4.12
1339 1343 0.697854 AGGGTCTGACCACTTTGGGT 60.698 55.000 26.94 0.00 43.37 4.51
1349 1353 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
1350 1354 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
1351 1355 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
1352 1356 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
1353 1357 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
1354 1358 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
1355 1359 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
1356 1360 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
1357 1361 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
1358 1362 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
1359 1363 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
1360 1364 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
1361 1365 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
1362 1366 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
1363 1367 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
1364 1368 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
1365 1369 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
1366 1370 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
1367 1371 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
1368 1372 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
1369 1373 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
1370 1374 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
1371 1375 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
1372 1376 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
1373 1377 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
1374 1378 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
1375 1379 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
1387 1391 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
1388 1392 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
1389 1393 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
1390 1394 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
1391 1395 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
1392 1396 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
1393 1397 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
1394 1398 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
1395 1399 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
1396 1400 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
1397 1401 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
1398 1402 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
1399 1403 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
1400 1404 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
1401 1405 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
1402 1406 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
1403 1407 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
1404 1408 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
1405 1409 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
1406 1410 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
1407 1411 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
1408 1412 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
1420 1424 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
1421 1425 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
1422 1426 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
1423 1427 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
1424 1428 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
1425 1429 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
1426 1430 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
1427 1431 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
1428 1432 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
1429 1433 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
1430 1434 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
1431 1435 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
1432 1436 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
1433 1437 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
1434 1438 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
1435 1439 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
1439 1443 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
1440 1444 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
1441 1445 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
1442 1446 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
1443 1447 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
1444 1448 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
1445 1449 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
1446 1450 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
1458 1462 4.928981 AGGCTCCCCTTCACAGAT 57.071 55.556 0.00 0.00 38.74 2.90
1459 1463 3.111265 AGGCTCCCCTTCACAGATT 57.889 52.632 0.00 0.00 38.74 2.40
1460 1464 0.622665 AGGCTCCCCTTCACAGATTG 59.377 55.000 0.00 0.00 38.74 2.67
1461 1465 0.329596 GGCTCCCCTTCACAGATTGT 59.670 55.000 0.00 0.00 0.00 2.71
1462 1466 1.272147 GGCTCCCCTTCACAGATTGTT 60.272 52.381 0.00 0.00 0.00 2.83
1463 1467 2.519013 GCTCCCCTTCACAGATTGTTT 58.481 47.619 0.00 0.00 0.00 2.83
1464 1468 2.489722 GCTCCCCTTCACAGATTGTTTC 59.510 50.000 0.00 0.00 0.00 2.78
1465 1469 3.084786 CTCCCCTTCACAGATTGTTTCC 58.915 50.000 0.00 0.00 0.00 3.13
1466 1470 2.171003 CCCCTTCACAGATTGTTTCCC 58.829 52.381 0.00 0.00 0.00 3.97
1467 1471 1.812571 CCCTTCACAGATTGTTTCCCG 59.187 52.381 0.00 0.00 0.00 5.14
1468 1472 1.200020 CCTTCACAGATTGTTTCCCGC 59.800 52.381 0.00 0.00 0.00 6.13
1469 1473 1.879380 CTTCACAGATTGTTTCCCGCA 59.121 47.619 0.00 0.00 0.00 5.69
1470 1474 1.234821 TCACAGATTGTTTCCCGCAC 58.765 50.000 0.00 0.00 0.00 5.34
1471 1475 1.202758 TCACAGATTGTTTCCCGCACT 60.203 47.619 0.00 0.00 0.00 4.40
1472 1476 2.037902 TCACAGATTGTTTCCCGCACTA 59.962 45.455 0.00 0.00 0.00 2.74
1473 1477 2.159627 CACAGATTGTTTCCCGCACTAC 59.840 50.000 0.00 0.00 0.00 2.73
1474 1478 2.224426 ACAGATTGTTTCCCGCACTACA 60.224 45.455 0.00 0.00 0.00 2.74
1475 1479 2.416547 CAGATTGTTTCCCGCACTACAG 59.583 50.000 0.00 0.00 0.00 2.74
1623 1628 2.200373 AAAGTTGGGATCGAAGGTGG 57.800 50.000 0.00 0.00 0.00 4.61
1722 1929 5.529581 AGTTTTGTGTTACCAATTGGAGG 57.470 39.130 31.22 4.97 38.94 4.30
2057 2270 5.297278 TGGTTTAGCAACGTTAAGTGTCATT 59.703 36.000 0.00 0.00 33.13 2.57
2182 2400 8.852135 GCTAGAGGAGAAGTATAAGCTTTAGAA 58.148 37.037 3.20 0.00 0.00 2.10
2647 2896 5.406780 GGATACTCCGATGCATCTAAAGTTG 59.593 44.000 23.73 6.81 0.00 3.16
2698 2947 0.392193 AGCTTGAACGCTGCTGCTAT 60.392 50.000 14.03 1.81 39.16 2.97
2737 2986 0.865769 GACGTGCCTGTCGACAAATT 59.134 50.000 20.49 0.57 0.00 1.82
2757 3006 2.481289 AAACTTGAGCCTGCCTCTAC 57.519 50.000 0.00 0.00 41.35 2.59
2856 3106 7.124599 TGGATACTTGGATGCATTTGAATTTCT 59.875 33.333 0.00 0.00 37.61 2.52
2862 3112 9.252962 CTTGGATGCATTTGAATTTCTAATACC 57.747 33.333 0.00 7.88 0.00 2.73
2864 3114 7.284261 TGGATGCATTTGAATTTCTAATACCGA 59.716 33.333 0.00 0.00 0.00 4.69
3002 3451 3.497332 ACTTGGTCTACTGTGCTAGACA 58.503 45.455 11.64 0.00 43.15 3.41
3015 3464 4.695455 TGTGCTAGACAAATAAGTCCTTGC 59.305 41.667 0.00 0.00 39.34 4.01
3074 3525 2.019249 TGCTGGATGTATGCTTGCTTC 58.981 47.619 0.00 0.00 0.00 3.86
3130 3584 6.183360 GGAACTGAGTATTGTTATGTGCCTTC 60.183 42.308 0.00 0.00 0.00 3.46
3154 3608 4.430137 TGTTTCAATGAGAAGCAGATGC 57.570 40.909 0.00 0.00 41.69 3.91
3174 3628 5.557576 TGCTAATATGATGTCTTCTGCCT 57.442 39.130 0.00 0.00 0.00 4.75
3270 3731 9.855361 CAGTCGCTGTGAATAAGAAATATAAAG 57.145 33.333 0.00 0.00 0.00 1.85
3305 3766 6.215121 TGTGGAATTACTGAAATGTTTGCTG 58.785 36.000 0.00 0.00 0.00 4.41
3314 3775 7.333528 ACTGAAATGTTTGCTGTTTCTAAGA 57.666 32.000 0.00 0.00 33.99 2.10
3389 3850 4.559862 AGTTCTTCGTCCTTTGATCCAT 57.440 40.909 0.00 0.00 0.00 3.41
3461 3922 3.039452 TGCTTGGCATGTGACACAT 57.961 47.368 15.48 15.48 39.91 3.21
3521 3982 8.103305 ACATTACAAGATTAATCTCACACAGGT 58.897 33.333 18.19 9.00 35.76 4.00
3554 4015 8.954834 ATTATGCCCATTATCCACAAATAAGA 57.045 30.769 0.00 0.00 0.00 2.10
3559 4020 6.716628 GCCCATTATCCACAAATAAGATCTCA 59.283 38.462 0.00 0.00 0.00 3.27
3560 4021 7.308830 GCCCATTATCCACAAATAAGATCTCAC 60.309 40.741 0.00 0.00 0.00 3.51
3566 4027 6.330278 TCCACAAATAAGATCTCACGTACAG 58.670 40.000 0.00 0.00 0.00 2.74
3567 4028 6.071560 TCCACAAATAAGATCTCACGTACAGT 60.072 38.462 0.00 0.00 0.00 3.55
3568 4029 6.590292 CCACAAATAAGATCTCACGTACAGTT 59.410 38.462 0.00 0.00 0.00 3.16
3570 4031 7.328493 CACAAATAAGATCTCACGTACAGTTGA 59.672 37.037 0.00 0.00 0.00 3.18
3573 4034 9.436957 AAATAAGATCTCACGTACAGTTGAAAT 57.563 29.630 0.00 0.00 0.00 2.17
3574 4035 6.712241 AAGATCTCACGTACAGTTGAAATG 57.288 37.500 0.00 0.00 0.00 2.32
3575 4036 6.025749 AGATCTCACGTACAGTTGAAATGA 57.974 37.500 0.00 0.00 0.00 2.57
3576 4037 6.096036 AGATCTCACGTACAGTTGAAATGAG 58.904 40.000 0.00 0.00 34.68 2.90
3577 4038 5.196341 TCTCACGTACAGTTGAAATGAGT 57.804 39.130 0.00 0.00 34.90 3.41
3578 4039 5.597806 TCTCACGTACAGTTGAAATGAGTT 58.402 37.500 0.00 0.00 34.90 3.01
3579 4040 5.690409 TCTCACGTACAGTTGAAATGAGTTC 59.310 40.000 0.00 0.00 34.90 3.01
3580 4041 5.353111 TCACGTACAGTTGAAATGAGTTCA 58.647 37.500 0.00 0.00 44.74 3.18
3680 4207 3.543680 ATAGTGACCATCGGGACAAAG 57.456 47.619 0.00 0.00 40.50 2.77
3710 4238 2.939022 GACAACAGTGCTCCACGC 59.061 61.111 0.00 0.00 39.64 5.34
3771 4299 3.181447 ACACATGGGAGCTCTTATGATGG 60.181 47.826 26.48 19.44 0.00 3.51
3781 4309 3.565902 GCTCTTATGATGGCACTAAACCC 59.434 47.826 0.00 0.00 0.00 4.11
3783 4311 5.036117 TCTTATGATGGCACTAAACCCTC 57.964 43.478 0.00 0.00 0.00 4.30
3786 4314 1.429148 GATGGCACTAAACCCTCGCG 61.429 60.000 0.00 0.00 0.00 5.87
3791 4319 3.195698 CTAAACCCTCGCGCCAGC 61.196 66.667 0.00 0.00 40.74 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.222389 CCCTAATTCTAGAGCTTGTGATGAG 58.778 44.000 0.00 0.00 0.00 2.90
2 3 5.453903 GCCCTAATTCTAGAGCTTGTGATGA 60.454 44.000 0.00 0.00 0.00 2.92
3 4 4.754114 GCCCTAATTCTAGAGCTTGTGATG 59.246 45.833 0.00 0.00 0.00 3.07
4 5 4.657969 AGCCCTAATTCTAGAGCTTGTGAT 59.342 41.667 0.00 0.00 35.83 3.06
5 6 4.033709 AGCCCTAATTCTAGAGCTTGTGA 58.966 43.478 0.00 0.00 35.83 3.58
6 7 4.125703 CAGCCCTAATTCTAGAGCTTGTG 58.874 47.826 0.00 0.00 37.12 3.33
7 8 3.135530 CCAGCCCTAATTCTAGAGCTTGT 59.864 47.826 0.00 0.00 37.12 3.16
8 9 3.389329 TCCAGCCCTAATTCTAGAGCTTG 59.611 47.826 0.00 0.00 37.12 4.01
9 10 3.658725 TCCAGCCCTAATTCTAGAGCTT 58.341 45.455 0.00 0.00 37.12 3.74
10 11 3.336509 TCCAGCCCTAATTCTAGAGCT 57.663 47.619 0.00 0.00 39.65 4.09
11 12 4.632327 ATTCCAGCCCTAATTCTAGAGC 57.368 45.455 0.00 0.00 0.00 4.09
12 13 5.011125 TCGAATTCCAGCCCTAATTCTAGAG 59.989 44.000 0.00 0.00 39.08 2.43
13 14 4.899457 TCGAATTCCAGCCCTAATTCTAGA 59.101 41.667 0.00 0.00 39.08 2.43
14 15 5.215252 TCGAATTCCAGCCCTAATTCTAG 57.785 43.478 0.00 0.00 39.08 2.43
15 16 4.503296 GCTCGAATTCCAGCCCTAATTCTA 60.503 45.833 13.51 3.05 39.08 2.10
16 17 3.745797 GCTCGAATTCCAGCCCTAATTCT 60.746 47.826 13.51 0.00 39.08 2.40
17 18 2.550180 GCTCGAATTCCAGCCCTAATTC 59.450 50.000 13.51 0.00 38.27 2.17
18 19 2.576615 GCTCGAATTCCAGCCCTAATT 58.423 47.619 13.51 0.00 0.00 1.40
19 20 2.262423 GCTCGAATTCCAGCCCTAAT 57.738 50.000 13.51 0.00 0.00 1.73
369 371 4.569943 AGTACTCGTGTAACTCGTTAGGA 58.430 43.478 0.00 0.00 31.75 2.94
432 434 4.508124 ACGAGTTGAGTCAAGCTTTAGTTG 59.492 41.667 5.62 0.00 0.00 3.16
474 476 0.179161 CTCGTGACTCGGCTCGAAAT 60.179 55.000 0.00 0.00 40.32 2.17
475 477 1.209383 CTCGTGACTCGGCTCGAAA 59.791 57.895 0.00 0.00 40.32 3.46
567 570 5.636123 TGGATCCTGGTTAAAAACTTAGCA 58.364 37.500 14.23 0.00 0.00 3.49
597 600 7.130099 TCCTGATAAGGTCACCAAATAGTCTA 58.870 38.462 0.00 0.00 32.22 2.59
603 606 5.255397 TGTTCCTGATAAGGTCACCAAAT 57.745 39.130 0.00 0.00 32.22 2.32
771 775 8.105197 TGTTGCAGATTGAGATGGCTATAATAT 58.895 33.333 0.00 0.00 0.00 1.28
844 848 6.486657 TGCTAGGACAAAATGCATTATACTCC 59.513 38.462 13.39 13.58 0.00 3.85
920 924 3.701040 CTCCCATTTCCAGTTTGGTATGG 59.299 47.826 17.44 17.44 43.67 2.74
1025 1029 2.624838 CAGCAATCTGTGGGTTCTGTTT 59.375 45.455 0.00 0.00 35.61 2.83
1113 1117 8.312669 AGTCCATGTTAGTAGAAATTCTAGCT 57.687 34.615 2.48 6.65 28.01 3.32
1261 1265 3.073678 GGTTGCCCCATTTGAAACAATC 58.926 45.455 0.00 0.00 0.00 2.67
1262 1266 2.710471 AGGTTGCCCCATTTGAAACAAT 59.290 40.909 0.00 0.00 34.66 2.71
1263 1267 2.122768 AGGTTGCCCCATTTGAAACAA 58.877 42.857 0.00 0.00 34.66 2.83
1264 1268 1.415659 CAGGTTGCCCCATTTGAAACA 59.584 47.619 0.00 0.00 34.66 2.83
1265 1269 1.270785 CCAGGTTGCCCCATTTGAAAC 60.271 52.381 0.00 0.00 34.66 2.78
1266 1270 1.055040 CCAGGTTGCCCCATTTGAAA 58.945 50.000 0.00 0.00 34.66 2.69
1267 1271 0.105246 ACCAGGTTGCCCCATTTGAA 60.105 50.000 0.00 0.00 34.66 2.69
1268 1272 0.831288 CACCAGGTTGCCCCATTTGA 60.831 55.000 0.00 0.00 34.66 2.69
1269 1273 1.672898 CACCAGGTTGCCCCATTTG 59.327 57.895 0.00 0.00 34.66 2.32
1270 1274 2.216331 GCACCAGGTTGCCCCATTT 61.216 57.895 0.00 0.00 36.42 2.32
1271 1275 2.604382 GCACCAGGTTGCCCCATT 60.604 61.111 0.00 0.00 36.42 3.16
1272 1276 3.242492 ATGCACCAGGTTGCCCCAT 62.242 57.895 10.46 0.00 42.25 4.00
1273 1277 3.913445 ATGCACCAGGTTGCCCCA 61.913 61.111 10.46 0.00 42.25 4.96
1274 1278 2.779742 TACATGCACCAGGTTGCCCC 62.780 60.000 10.46 0.00 42.25 5.80
1275 1279 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
1276 1280 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
1277 1281 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
1278 1282 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
1279 1283 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
1301 1305 3.551496 TTCCTGGACCCTGCGCAAG 62.551 63.158 13.05 4.91 43.44 4.01
1302 1306 3.126703 TTTCCTGGACCCTGCGCAA 62.127 57.895 13.05 0.00 0.00 4.85
1303 1307 3.551496 CTTTCCTGGACCCTGCGCA 62.551 63.158 10.98 10.98 0.00 6.09
1304 1308 2.747855 CTTTCCTGGACCCTGCGC 60.748 66.667 0.00 0.00 0.00 6.09
1305 1309 2.045926 CCTTTCCTGGACCCTGCG 60.046 66.667 0.00 0.00 0.00 5.18
1306 1310 2.356667 CCCTTTCCTGGACCCTGC 59.643 66.667 0.00 0.00 0.00 4.85
1307 1311 0.842467 AGACCCTTTCCTGGACCCTG 60.842 60.000 0.00 0.00 0.00 4.45
1308 1312 0.842467 CAGACCCTTTCCTGGACCCT 60.842 60.000 0.00 0.00 0.00 4.34
1309 1313 0.840722 TCAGACCCTTTCCTGGACCC 60.841 60.000 0.00 0.00 0.00 4.46
1310 1314 0.325272 GTCAGACCCTTTCCTGGACC 59.675 60.000 0.00 0.00 0.00 4.46
1311 1315 0.325272 GGTCAGACCCTTTCCTGGAC 59.675 60.000 8.65 0.00 30.04 4.02
1312 1316 0.104672 TGGTCAGACCCTTTCCTGGA 60.105 55.000 17.59 0.00 37.50 3.86
1313 1317 0.036875 GTGGTCAGACCCTTTCCTGG 59.963 60.000 17.59 0.00 37.50 4.45
1314 1318 1.059913 AGTGGTCAGACCCTTTCCTG 58.940 55.000 17.59 0.00 37.50 3.86
1315 1319 1.821088 AAGTGGTCAGACCCTTTCCT 58.179 50.000 17.59 2.40 37.50 3.36
1316 1320 2.230660 CAAAGTGGTCAGACCCTTTCC 58.769 52.381 23.30 7.37 36.95 3.13
1317 1321 2.230660 CCAAAGTGGTCAGACCCTTTC 58.769 52.381 23.30 11.17 36.95 2.62
1318 1322 1.133482 CCCAAAGTGGTCAGACCCTTT 60.133 52.381 21.61 21.61 38.45 3.11
1319 1323 0.478507 CCCAAAGTGGTCAGACCCTT 59.521 55.000 17.59 15.76 37.50 3.95
1320 1324 0.697854 ACCCAAAGTGGTCAGACCCT 60.698 55.000 17.59 10.65 37.50 4.34
1321 1325 1.844130 ACCCAAAGTGGTCAGACCC 59.156 57.895 17.59 8.45 37.50 4.46
1328 1332 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
1329 1333 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
1330 1334 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
1331 1335 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
1332 1336 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
1333 1337 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
1334 1338 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
1335 1339 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
1336 1340 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
1337 1341 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
1338 1342 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
1339 1343 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
1340 1344 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
1341 1345 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
1342 1346 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
1343 1347 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
1344 1348 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
1345 1349 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
1346 1350 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
1347 1351 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
1348 1352 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
1349 1353 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
1350 1354 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
1351 1355 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
1352 1356 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
1353 1357 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
1354 1358 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
1355 1359 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
1356 1360 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
1357 1361 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
1358 1362 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
1359 1363 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
1360 1364 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
1361 1365 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
1362 1366 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
1363 1367 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
1364 1368 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
1365 1369 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
1379 1383 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
1380 1384 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
1381 1385 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
1382 1386 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
1383 1387 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
1384 1388 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
1385 1389 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
1386 1390 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
1387 1391 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
1388 1392 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
1403 1407 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
1404 1408 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
1405 1409 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
1406 1410 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
1407 1411 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
1408 1412 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
1409 1413 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
1410 1414 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
1411 1415 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
1412 1416 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
1413 1417 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
1414 1418 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
1415 1419 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
1416 1420 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
1417 1421 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
1422 1426 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
1423 1427 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
1424 1428 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
1425 1429 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
1426 1430 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
1427 1431 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
1428 1432 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
1436 1440 4.033776 TGAAGGGGAGCCTTGGCG 62.034 66.667 5.95 0.00 0.00 5.69
1437 1441 2.361737 GTGAAGGGGAGCCTTGGC 60.362 66.667 2.97 2.97 0.00 4.52
1438 1442 1.001641 CTGTGAAGGGGAGCCTTGG 60.002 63.158 0.00 0.00 0.00 3.61
1439 1443 0.622665 ATCTGTGAAGGGGAGCCTTG 59.377 55.000 0.00 0.00 0.00 3.61
1440 1444 1.005215 CAATCTGTGAAGGGGAGCCTT 59.995 52.381 0.00 0.00 0.00 4.35
1441 1445 0.622665 CAATCTGTGAAGGGGAGCCT 59.377 55.000 0.00 0.00 0.00 4.58
1442 1446 0.329596 ACAATCTGTGAAGGGGAGCC 59.670 55.000 0.00 0.00 0.00 4.70
1443 1447 2.206576 AACAATCTGTGAAGGGGAGC 57.793 50.000 0.00 0.00 0.00 4.70
1444 1448 3.084786 GGAAACAATCTGTGAAGGGGAG 58.915 50.000 0.00 0.00 0.00 4.30
1445 1449 2.225017 GGGAAACAATCTGTGAAGGGGA 60.225 50.000 0.00 0.00 0.00 4.81
1446 1450 2.171003 GGGAAACAATCTGTGAAGGGG 58.829 52.381 0.00 0.00 0.00 4.79
1447 1451 1.812571 CGGGAAACAATCTGTGAAGGG 59.187 52.381 0.00 0.00 0.00 3.95
1448 1452 1.200020 GCGGGAAACAATCTGTGAAGG 59.800 52.381 0.00 0.00 0.00 3.46
1449 1453 1.879380 TGCGGGAAACAATCTGTGAAG 59.121 47.619 0.00 0.00 0.00 3.02
1450 1454 1.606668 GTGCGGGAAACAATCTGTGAA 59.393 47.619 0.00 0.00 0.00 3.18
1451 1455 1.202758 AGTGCGGGAAACAATCTGTGA 60.203 47.619 0.00 0.00 0.00 3.58
1452 1456 1.238439 AGTGCGGGAAACAATCTGTG 58.762 50.000 0.00 0.00 0.00 3.66
1453 1457 2.224426 TGTAGTGCGGGAAACAATCTGT 60.224 45.455 0.00 0.00 0.00 3.41
1454 1458 2.416547 CTGTAGTGCGGGAAACAATCTG 59.583 50.000 0.00 0.00 0.00 2.90
1455 1459 2.301870 TCTGTAGTGCGGGAAACAATCT 59.698 45.455 0.00 0.00 0.00 2.40
1456 1460 2.695359 TCTGTAGTGCGGGAAACAATC 58.305 47.619 0.00 0.00 0.00 2.67
1457 1461 2.851263 TCTGTAGTGCGGGAAACAAT 57.149 45.000 0.00 0.00 0.00 2.71
1458 1462 2.811431 CAATCTGTAGTGCGGGAAACAA 59.189 45.455 0.00 0.00 0.00 2.83
1459 1463 2.224426 ACAATCTGTAGTGCGGGAAACA 60.224 45.455 0.00 0.00 0.00 2.83
1460 1464 2.423577 ACAATCTGTAGTGCGGGAAAC 58.576 47.619 0.00 0.00 0.00 2.78
1461 1465 2.851263 ACAATCTGTAGTGCGGGAAA 57.149 45.000 0.00 0.00 0.00 3.13
1462 1466 2.851263 AACAATCTGTAGTGCGGGAA 57.149 45.000 0.00 0.00 0.00 3.97
1463 1467 2.037902 TGAAACAATCTGTAGTGCGGGA 59.962 45.455 0.00 0.00 0.00 5.14
1464 1468 2.422597 TGAAACAATCTGTAGTGCGGG 58.577 47.619 0.00 0.00 0.00 6.13
1465 1469 4.481930 TTTGAAACAATCTGTAGTGCGG 57.518 40.909 0.00 0.00 0.00 5.69
1466 1470 8.673626 AATTATTTGAAACAATCTGTAGTGCG 57.326 30.769 0.00 0.00 0.00 5.34
1467 1471 9.624697 TGAATTATTTGAAACAATCTGTAGTGC 57.375 29.630 0.00 0.00 0.00 4.40
1595 1599 7.499232 ACCTTCGATCCCAACTTTTATGATTAG 59.501 37.037 0.00 0.00 0.00 1.73
1886 2093 2.361757 CAGCATCACCAACACCTCAAAA 59.638 45.455 0.00 0.00 0.00 2.44
1933 2140 8.139350 CACACATATTTGCATACAAGAATCCAT 58.861 33.333 0.00 0.00 37.04 3.41
2057 2270 4.762765 ACCATAAACATAAGTCGGTTGCAA 59.237 37.500 0.00 0.00 0.00 4.08
2647 2896 7.865706 TTTAGAGCCTTCTTGACCATATTTC 57.134 36.000 0.00 0.00 34.79 2.17
2698 2947 1.473677 CCATGGATGCTCGCTTTGAAA 59.526 47.619 5.56 0.00 0.00 2.69
2737 2986 2.236395 GGTAGAGGCAGGCTCAAGTTTA 59.764 50.000 25.08 6.30 0.00 2.01
2757 3006 1.417890 ACCAAGTCACCTTCACTGAGG 59.582 52.381 0.00 0.00 42.75 3.86
2856 3106 2.762327 AGAGCCCTTTTCGTCGGTATTA 59.238 45.455 0.00 0.00 0.00 0.98
2862 3112 4.403453 CATTTTTAGAGCCCTTTTCGTCG 58.597 43.478 0.00 0.00 0.00 5.12
2864 3114 4.022329 CACCATTTTTAGAGCCCTTTTCGT 60.022 41.667 0.00 0.00 0.00 3.85
3074 3525 3.101209 CAACATCCATCCGGTGCG 58.899 61.111 0.00 0.00 0.00 5.34
3130 3584 4.934075 TCTGCTTCTCATTGAAACATCG 57.066 40.909 0.00 0.00 31.33 3.84
3154 3608 7.665690 AGTACAGGCAGAAGACATCATATTAG 58.334 38.462 0.00 0.00 0.00 1.73
3161 3615 4.037446 CCTAGAGTACAGGCAGAAGACATC 59.963 50.000 0.00 0.00 0.00 3.06
3174 3628 8.506196 AAATAATAAGCCATCCCTAGAGTACA 57.494 34.615 0.00 0.00 0.00 2.90
3270 3731 4.935808 CAGTAATTCCACAGTAGGGACAAC 59.064 45.833 0.00 0.00 33.18 3.32
3314 3775 8.357402 GGGTGACACTTGTTAGTTTATTTTGAT 58.643 33.333 5.39 0.00 30.26 2.57
3337 3798 9.943466 GCAAAAATACACTTTGAACCAAGGGGT 62.943 40.741 2.44 2.44 40.15 4.95
3408 3869 5.221621 GCAACTAGCCTGAATCTAGAGGAAT 60.222 44.000 0.00 0.00 37.53 3.01
3455 3916 8.932945 TTGAAATATCAGACTCTGTATGTGTC 57.067 34.615 5.94 3.26 36.78 3.67
3461 3922 9.424319 GTTTCACTTGAAATATCAGACTCTGTA 57.576 33.333 7.63 0.00 44.69 2.74
3521 3982 5.434708 TGGATAATGGGCATAATAGGGCATA 59.565 40.000 0.19 0.00 0.00 3.14
3554 4015 5.784177 ACTCATTTCAACTGTACGTGAGAT 58.216 37.500 0.00 0.00 36.15 2.75
3573 4034 9.725019 ACATGAATTATTACAGTCTTGAACTCA 57.275 29.630 0.00 0.00 35.45 3.41
3596 4123 7.410174 TGAACTCATTTCCCCTGTATAAACAT 58.590 34.615 0.00 0.00 31.89 2.71
3660 4187 3.104512 TCTTTGTCCCGATGGTCACTAT 58.895 45.455 0.00 0.00 28.93 2.12
3661 4188 2.531771 TCTTTGTCCCGATGGTCACTA 58.468 47.619 0.00 0.00 28.93 2.74
3680 4207 4.201724 GCACTGTTGTCGGTCAGATAAATC 60.202 45.833 0.00 0.00 35.84 2.17
3739 4267 4.666512 AGCTCCCATGTGTAGAAATTTGT 58.333 39.130 0.00 0.00 0.00 2.83
3751 4279 2.224719 GCCATCATAAGAGCTCCCATGT 60.225 50.000 19.36 8.74 0.00 3.21
3755 4283 1.419387 AGTGCCATCATAAGAGCTCCC 59.581 52.381 10.93 0.00 0.00 4.30
3756 4284 2.926778 AGTGCCATCATAAGAGCTCC 57.073 50.000 10.93 0.00 0.00 4.70
3771 4299 3.497031 GGCGCGAGGGTTTAGTGC 61.497 66.667 12.10 0.00 40.30 4.40


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

AutoCloner maintained by Alex Coulton.