Multiple sequence alignment - TraesCS5A01G219100

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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 TraesCS5A01G219100 chr5A 100.000 3668 0 0 1 3668 436332550 436328883 0.000000e+00 6774.0
1 TraesCS5A01G219100 chr5A 85.573 506 54 13 3163 3668 436548644 436549130 2.530000e-141 512.0
2 TraesCS5A01G219100 chr5A 80.804 448 50 12 3131 3559 436374258 436374688 5.910000e-83 318.0
3 TraesCS5A01G219100 chr5A 95.082 122 6 0 1411 1532 611023305 611023184 3.740000e-45 193.0
4 TraesCS5A01G219100 chr5A 89.552 134 9 3 823 951 328945746 328945879 8.150000e-37 165.0
5 TraesCS5A01G219100 chr5A 92.857 112 8 0 3557 3668 436353445 436353556 2.930000e-36 163.0
6 TraesCS5A01G219100 chr5A 95.652 92 2 2 735 825 436331726 436331816 2.950000e-31 147.0
7 TraesCS5A01G219100 chr5A 83.673 98 12 4 733 828 491293618 491293713 5.050000e-14 89.8
8 TraesCS5A01G219100 chr5A 83.696 92 10 4 735 824 491293710 491293622 8.440000e-12 82.4
9 TraesCS5A01G219100 chr5A 100.000 28 0 0 714 741 346189472 346189499 7.000000e-03 52.8
10 TraesCS5A01G219100 chr5D 90.072 1380 96 16 19 1381 335051953 335050598 0.000000e+00 1751.0
11 TraesCS5A01G219100 chr5D 89.897 1168 65 24 1538 2674 335050461 335049316 0.000000e+00 1454.0
12 TraesCS5A01G219100 chr5D 84.645 788 81 25 2904 3668 334970253 334969483 0.000000e+00 749.0
13 TraesCS5A01G219100 chr5D 88.641 537 52 8 3134 3668 335121197 335121726 0.000000e+00 645.0
14 TraesCS5A01G219100 chr5D 82.839 775 62 36 2936 3668 334991236 334990491 2.400000e-176 628.0
15 TraesCS5A01G219100 chr5D 83.179 541 67 19 3133 3668 335087076 335087597 1.190000e-129 473.0
16 TraesCS5A01G219100 chr5D 82.366 448 51 14 3134 3559 335060610 335061051 7.490000e-97 364.0
17 TraesCS5A01G219100 chr5D 83.256 215 15 11 2684 2894 335049141 335048944 1.050000e-40 178.0
18 TraesCS5A01G219100 chr5D 93.750 112 7 0 3557 3668 335061134 335061245 6.300000e-38 169.0
19 TraesCS5A01G219100 chr5D 87.912 91 8 2 735 825 335051152 335051239 1.800000e-18 104.0
20 TraesCS5A01G219100 chr5D 100.000 28 0 0 714 741 259536839 259536812 7.000000e-03 52.8
21 TraesCS5A01G219100 chr5B 89.543 1138 72 27 1546 2671 391828464 391827362 0.000000e+00 1399.0
22 TraesCS5A01G219100 chr5B 84.016 1026 92 36 2691 3668 391827197 391826196 0.000000e+00 920.0
23 TraesCS5A01G219100 chr5B 83.700 546 48 16 3134 3668 392118611 392119126 9.220000e-131 477.0
24 TraesCS5A01G219100 chr5B 81.857 474 35 25 1 465 391829752 391829321 5.830000e-93 351.0
25 TraesCS5A01G219100 chr5B 82.143 84 11 3 736 818 272191660 272191580 6.570000e-08 69.4
26 TraesCS5A01G219100 chr5B 100.000 28 0 0 714 741 294564196 294564223 7.000000e-03 52.8
27 TraesCS5A01G219100 chr7B 85.845 438 45 9 3134 3559 141009018 141008586 2.010000e-122 449.0
28 TraesCS5A01G219100 chr7B 94.488 127 6 1 1415 1541 5920135 5920260 1.040000e-45 195.0
29 TraesCS5A01G219100 chr7B 84.848 165 16 7 796 954 162140866 162140705 1.360000e-34 158.0
30 TraesCS5A01G219100 chr7B 100.000 31 0 0 715 745 464539973 464539943 1.420000e-04 58.4
31 TraesCS5A01G219100 chr7D 85.383 431 49 10 3134 3559 175662168 175661747 5.630000e-118 435.0
32 TraesCS5A01G219100 chr7A 83.893 447 46 12 3134 3559 177344732 177344291 1.590000e-108 403.0
33 TraesCS5A01G219100 chr2A 95.968 124 4 1 1408 1531 502330486 502330364 2.230000e-47 200.0
34 TraesCS5A01G219100 chr2A 96.639 119 4 0 1413 1531 78848938 78848820 8.030000e-47 198.0
35 TraesCS5A01G219100 chr2A 89.552 134 9 3 823 951 141506451 141506318 8.150000e-37 165.0
36 TraesCS5A01G219100 chr6D 95.161 124 4 2 1408 1530 287026020 287025898 1.040000e-45 195.0
37 TraesCS5A01G219100 chr4A 95.122 123 6 0 1408 1530 506712528 506712650 1.040000e-45 195.0
38 TraesCS5A01G219100 chr4A 86.667 165 13 7 798 954 93926781 93926944 1.350000e-39 174.0
39 TraesCS5A01G219100 chr3D 94.488 127 6 1 1412 1537 489163960 489164086 1.040000e-45 195.0
40 TraesCS5A01G219100 chr3B 94.400 125 7 0 1415 1539 345712332 345712456 3.740000e-45 193.0
41 TraesCS5A01G219100 chr2B 92.424 132 10 0 1415 1546 174395882 174395751 4.840000e-44 189.0
42 TraesCS5A01G219100 chr2B 87.234 141 12 4 823 958 190023024 190022885 4.900000e-34 156.0
43 TraesCS5A01G219100 chr4B 89.630 135 9 3 823 952 106227428 106227562 2.270000e-37 167.0
44 TraesCS5A01G219100 chr2D 89.552 134 9 3 823 951 79056186 79056319 8.150000e-37 165.0
45 TraesCS5A01G219100 chr4D 86.986 146 11 7 813 952 392514719 392514576 1.360000e-34 158.0
46 TraesCS5A01G219100 chr4D 84.444 90 7 5 736 824 467443690 467443773 8.440000e-12 82.4
47 TraesCS5A01G219100 chr1D 90.110 91 5 3 734 824 103225921 103225835 8.320000e-22 115.0
48 TraesCS5A01G219100 chr1D 86.170 94 9 3 732 825 103225831 103225920 8.380000e-17 99.0
49 TraesCS5A01G219100 chr1A 100.000 36 0 0 3491 3526 506474112 506474077 2.360000e-07 67.6
50 TraesCS5A01G219100 chr1A 97.297 37 1 0 3490 3526 506489257 506489221 3.060000e-06 63.9


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 TraesCS5A01G219100 chr5A 436328883 436332550 3667 True 6774.000000 6774 100.000000 1 3668 1 chr5A.!!$R1 3667
1 TraesCS5A01G219100 chr5D 335048944 335051953 3009 True 1127.666667 1751 87.741667 19 2894 3 chr5D.!!$R4 2875
2 TraesCS5A01G219100 chr5D 334969483 334970253 770 True 749.000000 749 84.645000 2904 3668 1 chr5D.!!$R2 764
3 TraesCS5A01G219100 chr5D 335121197 335121726 529 False 645.000000 645 88.641000 3134 3668 1 chr5D.!!$F3 534
4 TraesCS5A01G219100 chr5D 334990491 334991236 745 True 628.000000 628 82.839000 2936 3668 1 chr5D.!!$R3 732
5 TraesCS5A01G219100 chr5D 335087076 335087597 521 False 473.000000 473 83.179000 3133 3668 1 chr5D.!!$F2 535
6 TraesCS5A01G219100 chr5D 335060610 335061245 635 False 266.500000 364 88.058000 3134 3668 2 chr5D.!!$F4 534
7 TraesCS5A01G219100 chr5B 391826196 391829752 3556 True 890.000000 1399 85.138667 1 3668 3 chr5B.!!$R2 3667
8 TraesCS5A01G219100 chr5B 392118611 392119126 515 False 477.000000 477 83.700000 3134 3668 1 chr5B.!!$F2 534

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
403 407 0.398318 GTGGAGGAGAGCAAAGGTGT 59.602 55.000 0.00 0.00 0.00 4.16 F
1195 1387 1.068541 GCGTTGACCATTCCCTTCAAC 60.069 52.381 4.02 4.02 43.75 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1343 1535 0.036199 AGTCTGTCTACGCCGACTCT 60.036 55.0 0.0 0.96 31.51 3.24 R
2690 2982 0.167470 CCATTGCTCTTGACGCACAG 59.833 55.0 0.0 0.00 37.07 3.66 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
43 44 7.824289 CACATTACTGAATTCTTCTTGTCCCTA 59.176 37.037 7.05 0.00 0.00 3.53
44 45 8.552296 ACATTACTGAATTCTTCTTGTCCCTAT 58.448 33.333 7.05 0.00 0.00 2.57
45 46 9.401058 CATTACTGAATTCTTCTTGTCCCTATT 57.599 33.333 7.05 0.00 0.00 1.73
47 48 9.886132 TTACTGAATTCTTCTTGTCCCTATTAC 57.114 33.333 7.05 0.00 0.00 1.89
48 49 7.339482 ACTGAATTCTTCTTGTCCCTATTACC 58.661 38.462 7.05 0.00 0.00 2.85
49 50 7.182930 ACTGAATTCTTCTTGTCCCTATTACCT 59.817 37.037 7.05 0.00 0.00 3.08
64 65 9.629649 TCCCTATTACCTATACATTCTTGGAAT 57.370 33.333 0.00 0.00 0.00 3.01
203 205 6.918067 TCTGTGGTATGGAACTATGGATAG 57.082 41.667 0.00 0.00 36.46 2.08
224 226 8.580720 GGATAGTGTCTGCTGAAATCTCTAATA 58.419 37.037 0.00 0.00 0.00 0.98
233 235 6.994496 TGCTGAAATCTCTAATAACCAGATGG 59.006 38.462 0.00 0.00 42.17 3.51
294 296 7.823745 AGAAAGAAAGATTCTAAAGGCACAA 57.176 32.000 0.00 0.00 39.61 3.33
403 407 0.398318 GTGGAGGAGAGCAAAGGTGT 59.602 55.000 0.00 0.00 0.00 4.16
406 410 1.202818 GGAGGAGAGCAAAGGTGTTGT 60.203 52.381 0.00 0.00 0.00 3.32
411 415 3.489229 GGAGAGCAAAGGTGTTGTGTTTC 60.489 47.826 0.00 0.00 0.00 2.78
457 467 2.828877 TCGTGCAACTAAATATCCCCG 58.171 47.619 0.00 0.00 31.75 5.73
461 471 3.003378 GTGCAACTAAATATCCCCGCTTC 59.997 47.826 0.00 0.00 0.00 3.86
468 636 2.097110 ATATCCCCGCTTCACTGGTA 57.903 50.000 0.00 0.00 0.00 3.25
481 649 6.199154 CGCTTCACTGGTATGTAGTTATTCAG 59.801 42.308 0.00 0.00 0.00 3.02
482 650 7.265673 GCTTCACTGGTATGTAGTTATTCAGA 58.734 38.462 0.00 0.00 0.00 3.27
503 671 6.588756 TCAGAACGATTGTGGTAACTGATAAC 59.411 38.462 0.00 0.00 31.22 1.89
593 770 5.492895 TGATTTGGTATTTGCCGTCTAAGA 58.507 37.500 0.00 0.00 0.00 2.10
673 852 5.308014 TCAGCTGCTTTCTCAATTAAGTCA 58.692 37.500 9.47 0.00 0.00 3.41
745 925 2.268298 CGTTCACAAATACTCCCTCCG 58.732 52.381 0.00 0.00 0.00 4.63
748 928 1.829222 TCACAAATACTCCCTCCGTCC 59.171 52.381 0.00 0.00 0.00 4.79
749 929 1.831736 CACAAATACTCCCTCCGTCCT 59.168 52.381 0.00 0.00 0.00 3.85
763 943 3.514645 TCCGTCCTAAAATAAGTGTCGC 58.485 45.455 0.00 0.00 0.00 5.19
773 953 8.116753 CCTAAAATAAGTGTCGCTGATTTAGTG 58.883 37.037 8.84 3.66 37.29 2.74
774 954 5.470845 AATAAGTGTCGCTGATTTAGTGC 57.529 39.130 0.00 0.00 36.84 4.40
775 955 2.455674 AGTGTCGCTGATTTAGTGCA 57.544 45.000 0.00 0.00 36.84 4.57
815 995 3.306166 CAGCGACACTTATTTTAGGACGG 59.694 47.826 0.00 0.00 0.00 4.79
819 999 4.439968 GACACTTATTTTAGGACGGAGGG 58.560 47.826 0.00 0.00 0.00 4.30
894 1078 5.490139 AGTGTGTTTGTCACTCATTTCAG 57.510 39.130 0.00 0.00 46.27 3.02
899 1083 5.758296 GTGTTTGTCACTCATTTCAGTCCTA 59.242 40.000 0.00 0.00 43.13 2.94
900 1084 5.758296 TGTTTGTCACTCATTTCAGTCCTAC 59.242 40.000 0.00 0.00 0.00 3.18
901 1085 4.174411 TGTCACTCATTTCAGTCCTACG 57.826 45.455 0.00 0.00 0.00 3.51
902 1086 3.572682 TGTCACTCATTTCAGTCCTACGT 59.427 43.478 0.00 0.00 0.00 3.57
903 1087 4.763279 TGTCACTCATTTCAGTCCTACGTA 59.237 41.667 0.00 0.00 0.00 3.57
904 1088 5.106277 TGTCACTCATTTCAGTCCTACGTAG 60.106 44.000 15.92 15.92 0.00 3.51
944 1129 6.817765 AACATCTTGTATTTGTGAACGGAT 57.182 33.333 0.00 0.00 0.00 4.18
962 1147 3.700038 CGGATGGAGTAGTTAACTGACCT 59.300 47.826 18.56 10.69 39.07 3.85
1040 1225 4.218200 CACATTGGAAGGCAAGATGTAACA 59.782 41.667 0.00 0.00 30.39 2.41
1076 1261 8.604035 GTTACATTGAACTTCATATGTCGATGT 58.396 33.333 21.57 21.57 33.50 3.06
1112 1297 2.565367 GCAAAAAGCATCAAACTGCG 57.435 45.000 0.00 0.00 46.86 5.18
1140 1329 6.601613 TGATTATAGCAAGTTAACCCTGTTGG 59.398 38.462 0.88 0.00 41.37 3.77
1177 1369 9.840427 TTCTCCTTTATCTTTATTTTTCAAGCG 57.160 29.630 0.00 0.00 0.00 4.68
1179 1371 9.626045 CTCCTTTATCTTTATTTTTCAAGCGTT 57.374 29.630 0.00 0.00 0.00 4.84
1195 1387 1.068541 GCGTTGACCATTCCCTTCAAC 60.069 52.381 4.02 4.02 43.75 3.18
1198 1390 2.558359 GTTGACCATTCCCTTCAACAGG 59.442 50.000 8.46 0.00 45.60 4.00
1199 1391 1.177401 GACCATTCCCTTCAACAGGC 58.823 55.000 0.00 0.00 42.29 4.85
1224 1416 7.377928 GCACATCAAACTGCAGATGATTATAAC 59.622 37.037 26.30 15.70 43.28 1.89
1232 1424 7.701445 ACTGCAGATGATTATAACAAGCTTTC 58.299 34.615 23.35 0.00 0.00 2.62
1233 1425 7.337689 ACTGCAGATGATTATAACAAGCTTTCA 59.662 33.333 23.35 0.00 0.00 2.69
1288 1480 2.223144 TCCAGCAATTTTCACGTCTTCG 59.777 45.455 0.00 0.00 43.34 3.79
1305 1497 7.323177 CACGTCTTCGGTAGCTAAATTATCTAC 59.677 40.741 0.00 5.68 41.85 2.59
1306 1498 7.228308 ACGTCTTCGGTAGCTAAATTATCTACT 59.772 37.037 12.10 0.00 41.85 2.57
1307 1499 7.745594 CGTCTTCGGTAGCTAAATTATCTACTC 59.254 40.741 12.10 4.22 34.62 2.59
1321 1513 9.875708 AAATTATCTACTCCTCTCTACAGACAT 57.124 33.333 0.00 0.00 0.00 3.06
1322 1514 9.875708 AATTATCTACTCCTCTCTACAGACATT 57.124 33.333 0.00 0.00 0.00 2.71
1341 1533 8.087750 CAGACATTAATTAAGCCCTGACAAAAA 58.912 33.333 13.76 0.00 0.00 1.94
1342 1534 8.088365 AGACATTAATTAAGCCCTGACAAAAAC 58.912 33.333 3.94 0.00 0.00 2.43
1343 1535 7.731054 ACATTAATTAAGCCCTGACAAAAACA 58.269 30.769 3.94 0.00 0.00 2.83
1347 1540 2.736670 AGCCCTGACAAAAACAGAGT 57.263 45.000 0.00 0.00 37.54 3.24
1349 1542 1.264288 GCCCTGACAAAAACAGAGTCG 59.736 52.381 0.00 0.00 37.54 4.18
1384 1577 9.347240 AGACTTCATGTAAATGGATATTTGAGG 57.653 33.333 0.00 0.00 37.12 3.86
1425 1618 5.390087 TTGCTATCTAGTACTCCCTCTGT 57.610 43.478 0.00 0.00 0.00 3.41
1426 1619 4.975631 TGCTATCTAGTACTCCCTCTGTC 58.024 47.826 0.00 0.00 0.00 3.51
1428 1621 3.495434 ATCTAGTACTCCCTCTGTCCG 57.505 52.381 0.00 0.00 0.00 4.79
1429 1622 1.489649 TCTAGTACTCCCTCTGTCCGG 59.510 57.143 0.00 0.00 0.00 5.14
1430 1623 1.489649 CTAGTACTCCCTCTGTCCGGA 59.510 57.143 0.00 0.00 0.00 5.14
1432 1625 1.076677 AGTACTCCCTCTGTCCGGAAA 59.923 52.381 5.23 0.00 0.00 3.13
1433 1626 2.108970 GTACTCCCTCTGTCCGGAAAT 58.891 52.381 5.23 0.00 0.00 2.17
1435 1628 2.108970 ACTCCCTCTGTCCGGAAATAC 58.891 52.381 5.23 0.00 0.00 1.89
1436 1629 2.292323 ACTCCCTCTGTCCGGAAATACT 60.292 50.000 5.23 0.00 0.00 2.12
1438 1631 2.500098 TCCCTCTGTCCGGAAATACTTG 59.500 50.000 5.23 0.00 0.00 3.16
1439 1632 2.236395 CCCTCTGTCCGGAAATACTTGT 59.764 50.000 5.23 0.00 0.00 3.16
1440 1633 3.522553 CCTCTGTCCGGAAATACTTGTC 58.477 50.000 5.23 0.00 0.00 3.18
1441 1634 3.522553 CTCTGTCCGGAAATACTTGTCC 58.477 50.000 5.23 0.00 0.00 4.02
1442 1635 3.170717 TCTGTCCGGAAATACTTGTCCT 58.829 45.455 5.23 0.00 0.00 3.85
1443 1636 4.346730 TCTGTCCGGAAATACTTGTCCTA 58.653 43.478 5.23 0.00 0.00 2.94
1444 1637 4.401519 TCTGTCCGGAAATACTTGTCCTAG 59.598 45.833 5.23 0.00 0.00 3.02
1447 1640 5.246656 TGTCCGGAAATACTTGTCCTAGAAA 59.753 40.000 5.23 0.00 0.00 2.52
1448 1641 6.070424 TGTCCGGAAATACTTGTCCTAGAAAT 60.070 38.462 5.23 0.00 0.00 2.17
1449 1642 6.258068 GTCCGGAAATACTTGTCCTAGAAATG 59.742 42.308 5.23 0.00 0.00 2.32
1450 1643 5.527582 CCGGAAATACTTGTCCTAGAAATGG 59.472 44.000 0.00 0.00 0.00 3.16
1451 1644 6.113411 CGGAAATACTTGTCCTAGAAATGGT 58.887 40.000 0.00 0.00 0.00 3.55
1452 1645 6.598064 CGGAAATACTTGTCCTAGAAATGGTT 59.402 38.462 0.00 0.00 0.00 3.67
1453 1646 7.414098 CGGAAATACTTGTCCTAGAAATGGTTG 60.414 40.741 0.00 0.00 0.00 3.77
1454 1647 7.393515 GGAAATACTTGTCCTAGAAATGGTTGT 59.606 37.037 0.00 0.00 0.00 3.32
1456 1649 9.975218 AAATACTTGTCCTAGAAATGGTTGTAT 57.025 29.630 0.00 0.00 0.00 2.29
1457 1650 9.614792 AATACTTGTCCTAGAAATGGTTGTATC 57.385 33.333 0.00 0.00 0.00 2.24
1459 1652 8.375493 ACTTGTCCTAGAAATGGTTGTATCTA 57.625 34.615 0.00 0.00 0.00 1.98
1460 1653 8.478877 ACTTGTCCTAGAAATGGTTGTATCTAG 58.521 37.037 0.00 0.00 40.55 2.43
1461 1654 8.603898 TTGTCCTAGAAATGGTTGTATCTAGA 57.396 34.615 9.60 0.00 42.48 2.43
1462 1655 8.008513 TGTCCTAGAAATGGTTGTATCTAGAC 57.991 38.462 9.60 7.06 42.48 2.59
1463 1656 7.839705 TGTCCTAGAAATGGTTGTATCTAGACT 59.160 37.037 9.60 0.00 42.48 3.24
1464 1657 8.697292 GTCCTAGAAATGGTTGTATCTAGACTT 58.303 37.037 9.60 0.00 42.48 3.01
1465 1658 9.931698 TCCTAGAAATGGTTGTATCTAGACTTA 57.068 33.333 9.60 0.00 42.48 2.24
1517 1710 9.816354 ATCCATTTTTAAGACAAATATTTCCGG 57.184 29.630 0.00 0.00 0.00 5.14
1518 1711 9.026121 TCCATTTTTAAGACAAATATTTCCGGA 57.974 29.630 0.00 0.00 0.00 5.14
1616 1865 2.490903 AGATGTGCTGCATGGAAAAGTC 59.509 45.455 5.27 0.00 38.06 3.01
1661 1943 5.110598 TGCATTTCGATTTAAAGCATGCAT 58.889 33.333 21.98 4.57 37.56 3.96
1662 1944 5.581479 TGCATTTCGATTTAAAGCATGCATT 59.419 32.000 21.98 17.42 37.56 3.56
1663 1945 5.899696 GCATTTCGATTTAAAGCATGCATTG 59.100 36.000 21.98 8.13 33.25 2.82
1714 1996 6.529477 GTCCGAACTAGTTGACCTTTACATAC 59.471 42.308 14.14 0.00 0.00 2.39
1781 2068 3.510531 AGGTTGTTCTTTCCTTCCTCC 57.489 47.619 0.00 0.00 0.00 4.30
1782 2069 3.056832 AGGTTGTTCTTTCCTTCCTCCT 58.943 45.455 0.00 0.00 0.00 3.69
1783 2070 3.073209 AGGTTGTTCTTTCCTTCCTCCTC 59.927 47.826 0.00 0.00 0.00 3.71
1802 2089 5.749462 TCCTCATCTTTTCTCCTTTGATCC 58.251 41.667 0.00 0.00 0.00 3.36
1815 2102 4.522789 TCCTTTGATCCCTTTCCTTTTTCG 59.477 41.667 0.00 0.00 0.00 3.46
1829 2116 0.031994 TTTTCGCTTTTGCTCCTGCC 59.968 50.000 0.00 0.00 44.80 4.85
1949 2236 1.138069 TGCGCTAATGGATCGGAAAGA 59.862 47.619 9.73 0.00 0.00 2.52
1950 2237 1.795286 GCGCTAATGGATCGGAAAGAG 59.205 52.381 0.00 0.00 0.00 2.85
1951 2238 1.795286 CGCTAATGGATCGGAAAGAGC 59.205 52.381 0.00 0.00 33.78 4.09
1952 2239 2.546795 CGCTAATGGATCGGAAAGAGCT 60.547 50.000 0.00 0.00 35.20 4.09
1953 2240 3.063485 GCTAATGGATCGGAAAGAGCTC 58.937 50.000 5.27 5.27 35.20 4.09
1954 2241 3.493350 GCTAATGGATCGGAAAGAGCTCA 60.493 47.826 17.77 0.00 35.20 4.26
1955 2242 3.853355 AATGGATCGGAAAGAGCTCAT 57.147 42.857 17.77 0.00 35.20 2.90
1957 2244 2.392662 TGGATCGGAAAGAGCTCATCT 58.607 47.619 17.77 0.00 41.27 2.90
1958 2245 2.363680 TGGATCGGAAAGAGCTCATCTC 59.636 50.000 17.77 8.75 37.23 2.75
1959 2246 2.288763 GGATCGGAAAGAGCTCATCTCC 60.289 54.545 17.77 16.31 42.90 3.71
2015 2302 1.810606 CTCCCGTGCACTGACTGACT 61.811 60.000 16.19 0.00 0.00 3.41
2034 2321 4.081972 TGACTGTTTCAGTAGCATCTCTCC 60.082 45.833 2.29 0.00 45.44 3.71
2035 2322 4.093011 ACTGTTTCAGTAGCATCTCTCCT 58.907 43.478 0.27 0.00 43.46 3.69
2036 2323 4.159506 ACTGTTTCAGTAGCATCTCTCCTC 59.840 45.833 0.27 0.00 43.46 3.71
2053 2340 7.102346 TCTCTCCTCTTTCTTTCTATGCTTTG 58.898 38.462 0.00 0.00 0.00 2.77
2100 2390 2.095853 CACTGGCTTATAAACACAGGCG 59.904 50.000 12.57 0.00 35.89 5.52
2118 2408 1.081242 GTTGCATTGCACAGTCGGG 60.081 57.895 11.66 0.00 38.71 5.14
2157 2447 1.425412 TCGCTTGAAGTTTCGGCTAC 58.575 50.000 0.00 0.00 0.00 3.58
2187 2477 1.733912 TGGTAGAGTAGTGCGTACGTG 59.266 52.381 17.90 0.00 36.66 4.49
2195 2487 3.299977 TGCGTACGTGCAGGACCT 61.300 61.111 17.90 0.00 40.62 3.85
2197 2489 2.092882 GCGTACGTGCAGGACCTTC 61.093 63.158 17.90 0.00 34.15 3.46
2281 2573 1.646189 TTGTTTTTCCGTTTGCAGGC 58.354 45.000 0.00 0.00 0.00 4.85
2282 2574 0.532573 TGTTTTTCCGTTTGCAGGCA 59.467 45.000 0.00 0.00 0.00 4.75
2283 2575 1.208259 GTTTTTCCGTTTGCAGGCAG 58.792 50.000 0.00 0.00 0.00 4.85
2306 2598 1.202915 TGCAGCATGGGTTTTCAGAGA 60.203 47.619 0.00 0.00 35.86 3.10
2340 2632 1.039785 CGAGAGAGCCACCATCCAGA 61.040 60.000 0.00 0.00 0.00 3.86
2341 2633 1.198713 GAGAGAGCCACCATCCAGAA 58.801 55.000 0.00 0.00 0.00 3.02
2343 2635 1.198713 GAGAGCCACCATCCAGAAGA 58.801 55.000 0.00 0.00 0.00 2.87
2344 2636 0.908198 AGAGCCACCATCCAGAAGAC 59.092 55.000 0.00 0.00 0.00 3.01
2390 2682 2.125512 ATGAAGCGGCCTCGTGAC 60.126 61.111 0.00 0.00 38.89 3.67
2405 2697 2.126031 GACGGTGAGGACGAAGGC 60.126 66.667 0.00 0.00 34.93 4.35
2526 2818 0.889186 CCTGGACGGGTTCAAGGTTG 60.889 60.000 0.00 0.00 40.43 3.77
2532 2824 0.817634 CGGGTTCAAGGTTGTGAGCA 60.818 55.000 0.00 0.00 30.89 4.26
2574 2866 2.946762 GTTGACGAGCCACCTTGC 59.053 61.111 0.00 0.00 0.00 4.01
2578 2870 2.970974 GACGAGCCACCTTGCTTGC 61.971 63.158 0.00 0.00 45.08 4.01
2591 2883 3.062504 CCTTGCTTGCTTGTTTGTTTGTC 59.937 43.478 0.00 0.00 0.00 3.18
2593 2885 3.924144 TGCTTGCTTGTTTGTTTGTCTT 58.076 36.364 0.00 0.00 0.00 3.01
2615 2907 6.440965 TCTTTTTAGTTAGAGAAGAGAGGGGG 59.559 42.308 0.00 0.00 0.00 5.40
2647 2939 4.105486 GGTGTTTTTGTGCTCTTCAACTC 58.895 43.478 0.00 0.00 0.00 3.01
2671 2963 5.890424 TCTTTTTAACCGGAATAAGCCTG 57.110 39.130 9.46 0.12 0.00 4.85
2674 2966 6.372381 TCTTTTTAACCGGAATAAGCCTGTAC 59.628 38.462 9.46 0.00 0.00 2.90
2675 2967 4.822685 TTAACCGGAATAAGCCTGTACA 57.177 40.909 9.46 0.00 0.00 2.90
2676 2968 3.926058 AACCGGAATAAGCCTGTACAT 57.074 42.857 9.46 0.00 0.00 2.29
2678 2970 4.230745 ACCGGAATAAGCCTGTACATTT 57.769 40.909 9.46 0.00 0.00 2.32
2679 2971 3.945285 ACCGGAATAAGCCTGTACATTTG 59.055 43.478 9.46 0.00 0.00 2.32
2681 2973 3.376859 CGGAATAAGCCTGTACATTTGCA 59.623 43.478 12.81 0.00 0.00 4.08
2682 2974 4.142491 CGGAATAAGCCTGTACATTTGCAA 60.142 41.667 12.81 0.00 0.00 4.08
2685 2977 6.405731 GGAATAAGCCTGTACATTTGCAATGA 60.406 38.462 0.00 0.00 0.00 2.57
2688 2980 6.528537 AAGCCTGTACATTTGCAATGAATA 57.471 33.333 0.00 0.00 0.00 1.75
2690 2982 4.741676 GCCTGTACATTTGCAATGAATAGC 59.258 41.667 0.00 0.00 0.00 2.97
2691 2983 5.450965 GCCTGTACATTTGCAATGAATAGCT 60.451 40.000 0.00 0.00 0.00 3.32
2693 2985 6.405065 CCTGTACATTTGCAATGAATAGCTGT 60.405 38.462 0.00 0.00 0.00 4.40
2694 2986 6.324042 TGTACATTTGCAATGAATAGCTGTG 58.676 36.000 0.00 0.00 0.00 3.66
2695 2987 4.178540 ACATTTGCAATGAATAGCTGTGC 58.821 39.130 0.00 0.00 35.75 4.57
2764 3221 2.181975 CAATCCCTGGGTTTCAGCATT 58.818 47.619 13.56 0.00 42.05 3.56
2767 3224 0.890683 CCCTGGGTTTCAGCATTCAC 59.109 55.000 3.97 0.00 42.05 3.18
2806 3263 4.591321 TGGAGCCAGGAATTGAGTTTAT 57.409 40.909 0.00 0.00 0.00 1.40
2861 3322 5.733620 TCTGAACACGGTAAGGTCTTAAT 57.266 39.130 0.00 0.00 0.00 1.40
2862 3323 6.105397 TCTGAACACGGTAAGGTCTTAATT 57.895 37.500 0.00 0.00 0.00 1.40
2863 3324 6.527423 TCTGAACACGGTAAGGTCTTAATTT 58.473 36.000 0.00 0.00 0.00 1.82
2894 3355 5.237344 AGGCATTAGATCAAGAAACGTATGC 59.763 40.000 0.00 3.53 36.14 3.14
2897 3358 7.134815 GCATTAGATCAAGAAACGTATGCATT 58.865 34.615 3.54 0.00 36.70 3.56
2899 3360 9.803130 CATTAGATCAAGAAACGTATGCATTAG 57.197 33.333 3.54 1.52 0.00 1.73
2900 3361 9.764363 ATTAGATCAAGAAACGTATGCATTAGA 57.236 29.630 3.54 0.00 0.00 2.10
2901 3362 9.764363 TTAGATCAAGAAACGTATGCATTAGAT 57.236 29.630 3.54 0.00 0.00 1.98
2902 3363 8.304202 AGATCAAGAAACGTATGCATTAGATC 57.696 34.615 3.54 5.40 0.00 2.75
2962 3440 1.288419 CTTCCGCGTATGCACACACA 61.288 55.000 4.92 0.00 42.97 3.72
2963 3441 0.880718 TTCCGCGTATGCACACACAA 60.881 50.000 4.92 0.00 42.97 3.33
2964 3442 1.154488 CCGCGTATGCACACACAAC 60.154 57.895 4.92 0.00 42.97 3.32
2965 3443 1.567050 CGCGTATGCACACACAACA 59.433 52.632 7.86 0.00 42.97 3.33
2966 3444 0.721155 CGCGTATGCACACACAACAC 60.721 55.000 7.86 0.00 42.97 3.32
2982 3465 5.670097 CACAACACGTGTTTCTCTAAGATG 58.330 41.667 30.49 18.15 38.92 2.90
3020 3503 4.142773 CGCTAGAAACAAAGCCCGAATTTA 60.143 41.667 0.00 0.00 35.22 1.40
3021 3504 5.618195 CGCTAGAAACAAAGCCCGAATTTAA 60.618 40.000 0.00 0.00 35.22 1.52
3046 3529 2.571757 CTGCGCTTCTGGTCCGTA 59.428 61.111 9.73 0.00 0.00 4.02
3047 3530 1.805945 CTGCGCTTCTGGTCCGTAC 60.806 63.158 9.73 0.00 0.00 3.67
3048 3531 2.508663 GCGCTTCTGGTCCGTACC 60.509 66.667 0.00 0.00 46.98 3.34
3065 3548 2.490217 CGTAGGTGCTGGAGTCCG 59.510 66.667 4.30 0.44 0.00 4.79
3076 3560 2.586357 GAGTCCGCGGATGCTTCC 60.586 66.667 33.58 17.51 39.65 3.46
3083 3567 1.586154 CGCGGATGCTTCCCAACTTT 61.586 55.000 12.77 0.00 39.01 2.66
3085 3569 1.402852 GCGGATGCTTCCCAACTTTTC 60.403 52.381 12.77 0.00 39.01 2.29
3086 3570 2.162681 CGGATGCTTCCCAACTTTTCT 58.837 47.619 12.77 0.00 39.01 2.52
3087 3571 3.343617 CGGATGCTTCCCAACTTTTCTA 58.656 45.455 12.77 0.00 39.01 2.10
3088 3572 3.375299 CGGATGCTTCCCAACTTTTCTAG 59.625 47.826 12.77 0.00 39.01 2.43
3089 3573 4.589908 GGATGCTTCCCAACTTTTCTAGA 58.410 43.478 7.41 0.00 35.84 2.43
3092 3576 5.818678 TGCTTCCCAACTTTTCTAGAGTA 57.181 39.130 0.00 0.00 0.00 2.59
3112 3596 4.943705 AGTATCTGTTTGGCGTTTCATGAT 59.056 37.500 0.00 0.00 0.00 2.45
3114 3598 3.145286 TCTGTTTGGCGTTTCATGATGA 58.855 40.909 0.00 0.00 0.00 2.92
3115 3599 3.567585 TCTGTTTGGCGTTTCATGATGAA 59.432 39.130 3.29 3.29 34.03 2.57
3116 3600 3.899734 TGTTTGGCGTTTCATGATGAAG 58.100 40.909 8.01 0.00 37.70 3.02
3117 3601 2.634982 TTGGCGTTTCATGATGAAGC 57.365 45.000 11.39 11.39 37.70 3.86
3121 3605 1.474077 GCGTTTCATGATGAAGCCCTT 59.526 47.619 14.94 0.00 37.70 3.95
3128 3633 1.377202 GATGAAGCCCTTGTCCGCA 60.377 57.895 0.00 0.00 0.00 5.69
3129 3634 1.648467 GATGAAGCCCTTGTCCGCAC 61.648 60.000 0.00 0.00 0.00 5.34
3131 3636 4.250305 AAGCCCTTGTCCGCACGT 62.250 61.111 0.00 0.00 0.00 4.49
3137 3642 3.620300 CTTGTCCGCACGTCCGCTA 62.620 63.158 0.00 0.00 0.00 4.26
3154 3659 1.595466 CTACCTCGCTCCACGTAGAT 58.405 55.000 0.00 0.00 44.19 1.98
3160 3666 1.402968 TCGCTCCACGTAGATGGTAAC 59.597 52.381 0.00 0.00 44.19 2.50
3161 3667 1.535437 CGCTCCACGTAGATGGTAACC 60.535 57.143 0.00 0.00 40.95 2.85
3263 3782 0.818040 CGGCCTATAAACTGTGCCCC 60.818 60.000 0.00 0.00 38.92 5.80
3337 3876 8.293699 TCAGAAACTGTACTAGCAATCATCTA 57.706 34.615 0.00 0.00 32.61 1.98
3338 3877 8.409371 TCAGAAACTGTACTAGCAATCATCTAG 58.591 37.037 0.00 0.00 35.49 2.43
3339 3878 7.168972 CAGAAACTGTACTAGCAATCATCTAGC 59.831 40.741 0.00 0.00 37.60 3.42
3340 3879 5.461032 ACTGTACTAGCAATCATCTAGCC 57.539 43.478 0.00 0.00 37.60 3.93
3341 3880 4.022762 ACTGTACTAGCAATCATCTAGCCG 60.023 45.833 0.00 0.00 37.60 5.52
3342 3881 4.142038 TGTACTAGCAATCATCTAGCCGA 58.858 43.478 0.00 0.00 37.60 5.54
3343 3882 4.767409 TGTACTAGCAATCATCTAGCCGAT 59.233 41.667 0.00 0.00 37.60 4.18
3344 3883 4.881019 ACTAGCAATCATCTAGCCGATT 57.119 40.909 0.00 1.75 37.60 3.34
3345 3884 4.815269 ACTAGCAATCATCTAGCCGATTC 58.185 43.478 4.09 1.66 37.60 2.52
3346 3885 3.051081 AGCAATCATCTAGCCGATTCC 57.949 47.619 4.09 0.00 29.38 3.01
3354 3893 1.153168 TAGCCGATTCCTTGCCTGC 60.153 57.895 0.00 0.00 0.00 4.85
3377 3939 2.679059 GCAGCATCTGTAGCTTCCTTCA 60.679 50.000 0.00 0.00 41.14 3.02
3479 4047 2.829003 CTCGGCGCCAGGTCTCTA 60.829 66.667 28.98 1.21 0.00 2.43
3584 4237 3.815569 CTCGATCTGGGACGCGCTC 62.816 68.421 5.73 2.64 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 9.125026 GTCAATGAATTCCAAGAATGTATAGGT 57.875 33.333 2.27 0.00 0.00 3.08
47 48 9.347240 AGTCAATGAATTCCAAGAATGTATAGG 57.653 33.333 2.27 0.00 0.00 2.57
64 65 5.568825 GCCCTGTTAGTCACTAGTCAATGAA 60.569 44.000 0.00 0.00 0.00 2.57
139 141 7.440523 AGATTTAGACCACTCATTTTGTGAC 57.559 36.000 0.00 0.00 37.60 3.67
147 149 9.911788 AATTTGTCATAGATTTAGACCACTCAT 57.088 29.630 0.00 0.00 0.00 2.90
203 205 6.818644 TGGTTATTAGAGATTTCAGCAGACAC 59.181 38.462 0.00 0.00 0.00 3.67
261 263 9.696917 TTTAGAATCTTTCTTTCTTGCCAATTC 57.303 29.630 0.00 0.00 41.14 2.17
294 296 4.125703 GCTCATCGGATCTGAAATCTTGT 58.874 43.478 8.65 0.00 0.00 3.16
361 365 9.801873 CCACATTTGAGATAATACCGAAATTTT 57.198 29.630 0.00 0.00 0.00 1.82
411 415 9.965824 AACTCCACTAACAAATCTTAAACAATG 57.034 29.630 0.00 0.00 0.00 2.82
457 467 7.265673 TCTGAATAACTACATACCAGTGAAGC 58.734 38.462 0.00 0.00 0.00 3.86
461 471 7.255569 TCGTTCTGAATAACTACATACCAGTG 58.744 38.462 0.00 0.00 0.00 3.66
468 636 7.103641 ACCACAATCGTTCTGAATAACTACAT 58.896 34.615 0.00 0.00 0.00 2.29
481 649 6.672357 GCTGTTATCAGTTACCACAATCGTTC 60.672 42.308 2.85 0.00 43.05 3.95
482 650 5.121768 GCTGTTATCAGTTACCACAATCGTT 59.878 40.000 2.85 0.00 43.05 3.85
554 731 5.009010 ACCAAATCAGCACAACAGAAGTTAG 59.991 40.000 0.00 0.00 35.85 2.34
593 770 7.042797 ACTGTCAAAATCTACAAGTTTGCAT 57.957 32.000 0.00 0.00 41.53 3.96
718 898 3.522553 GAGTATTTGTGAACGGAGGGAG 58.477 50.000 0.00 0.00 0.00 4.30
719 899 2.235402 GGAGTATTTGTGAACGGAGGGA 59.765 50.000 0.00 0.00 0.00 4.20
745 925 6.663944 AATCAGCGACACTTATTTTAGGAC 57.336 37.500 0.00 0.00 0.00 3.85
748 928 7.636359 GCACTAAATCAGCGACACTTATTTTAG 59.364 37.037 0.00 0.00 34.69 1.85
749 929 7.118535 TGCACTAAATCAGCGACACTTATTTTA 59.881 33.333 0.00 0.00 34.69 1.52
763 943 5.565723 GCAAAGTTGTTGCACTAAATCAG 57.434 39.130 6.19 0.00 44.34 2.90
773 953 4.084900 GCTGATTTAGTGCAAAGTTGTTGC 60.085 41.667 4.12 4.12 45.11 4.17
774 954 4.146961 CGCTGATTTAGTGCAAAGTTGTTG 59.853 41.667 0.00 0.00 0.00 3.33
775 955 4.036262 TCGCTGATTTAGTGCAAAGTTGTT 59.964 37.500 0.00 0.00 36.84 2.83
844 1024 5.391449 CGTGTCTATATACACCCGATTCAG 58.609 45.833 13.93 0.00 45.66 3.02
853 1036 6.916387 ACACACTAATGCGTGTCTATATACAC 59.084 38.462 10.55 10.55 45.74 2.90
894 1078 8.743085 TGGATATAATATGGACTACGTAGGAC 57.257 38.462 25.63 17.62 0.00 3.85
939 1124 3.446516 GGTCAGTTAACTACTCCATCCGT 59.553 47.826 8.04 0.00 33.85 4.69
962 1147 7.610305 GGATGTGATCCTTGGTCTTTTAAACTA 59.390 37.037 0.00 0.00 46.19 2.24
1015 1200 1.134907 CATCTTGCCTTCCAATGTGGC 60.135 52.381 0.00 0.00 46.26 5.01
1029 1214 9.268268 TGTAACCTTTTAGACTGTTACATCTTG 57.732 33.333 10.02 0.00 44.68 3.02
1040 1225 8.974060 TGAAGTTCAATGTAACCTTTTAGACT 57.026 30.769 2.20 0.00 0.00 3.24
1069 1254 2.673368 GGAATTGTCTCCACACATCGAC 59.327 50.000 0.00 0.00 35.36 4.20
1076 1261 0.770499 TGCAGGGAATTGTCTCCACA 59.230 50.000 0.00 0.00 37.20 4.17
1112 1297 8.904099 ACAGGGTTAACTTGCTATAATCATAC 57.096 34.615 5.42 0.00 0.00 2.39
1159 1348 7.877003 TGGTCAACGCTTGAAAAATAAAGATA 58.123 30.769 2.65 0.00 42.15 1.98
1166 1358 4.306600 GGAATGGTCAACGCTTGAAAAAT 58.693 39.130 2.65 0.00 42.15 1.82
1179 1371 2.584835 CCTGTTGAAGGGAATGGTCA 57.415 50.000 0.00 0.00 43.15 4.02
1195 1387 1.241165 TCTGCAGTTTGATGTGCCTG 58.759 50.000 14.67 0.00 39.04 4.85
1198 1390 3.777465 ATCATCTGCAGTTTGATGTGC 57.223 42.857 24.43 0.00 40.46 4.57
1199 1391 8.400186 TGTTATAATCATCTGCAGTTTGATGTG 58.600 33.333 25.22 11.43 40.46 3.21
1224 1416 5.050567 GTCTGAGCCAATTTTTGAAAGCTTG 60.051 40.000 0.00 0.00 0.00 4.01
1232 1424 5.437289 TGTAGTGTCTGAGCCAATTTTTG 57.563 39.130 0.00 0.00 0.00 2.44
1233 1425 5.536161 ACATGTAGTGTCTGAGCCAATTTTT 59.464 36.000 0.00 0.00 35.77 1.94
1237 1429 3.988976 ACATGTAGTGTCTGAGCCAAT 57.011 42.857 0.00 0.00 35.77 3.16
1240 1432 1.734465 GCAACATGTAGTGTCTGAGCC 59.266 52.381 0.00 0.00 41.14 4.70
1288 1480 8.873186 AGAGAGGAGTAGATAATTTAGCTACC 57.127 38.462 22.08 15.47 46.05 3.18
1305 1497 7.870445 GGCTTAATTAATGTCTGTAGAGAGGAG 59.130 40.741 0.00 0.00 0.00 3.69
1306 1498 7.202011 GGGCTTAATTAATGTCTGTAGAGAGGA 60.202 40.741 0.00 0.00 0.00 3.71
1307 1499 6.931840 GGGCTTAATTAATGTCTGTAGAGAGG 59.068 42.308 0.00 0.00 0.00 3.69
1320 1512 8.189119 TCTGTTTTTGTCAGGGCTTAATTAAT 57.811 30.769 0.00 0.00 34.15 1.40
1321 1513 7.286775 ACTCTGTTTTTGTCAGGGCTTAATTAA 59.713 33.333 0.00 0.00 36.94 1.40
1322 1514 6.775629 ACTCTGTTTTTGTCAGGGCTTAATTA 59.224 34.615 0.00 0.00 36.94 1.40
1323 1515 5.598417 ACTCTGTTTTTGTCAGGGCTTAATT 59.402 36.000 0.00 0.00 36.94 1.40
1341 1533 0.321387 TCTGTCTACGCCGACTCTGT 60.321 55.000 0.00 0.00 35.00 3.41
1342 1534 0.097325 GTCTGTCTACGCCGACTCTG 59.903 60.000 0.00 0.00 35.00 3.35
1343 1535 0.036199 AGTCTGTCTACGCCGACTCT 60.036 55.000 0.00 0.96 31.51 3.24
1347 1540 1.132453 CATGAAGTCTGTCTACGCCGA 59.868 52.381 0.00 0.00 0.00 5.54
1349 1542 2.656560 ACATGAAGTCTGTCTACGCC 57.343 50.000 0.00 0.00 0.00 5.68
1384 1577 9.170584 GATAGCAAACTAACTGTTTTCTGTTTC 57.829 33.333 0.00 2.12 45.69 2.78
1400 1593 5.830991 CAGAGGGAGTACTAGATAGCAAACT 59.169 44.000 0.00 0.00 0.00 2.66
1425 1618 6.346096 CATTTCTAGGACAAGTATTTCCGGA 58.654 40.000 0.00 0.00 36.95 5.14
1426 1619 5.527582 CCATTTCTAGGACAAGTATTTCCGG 59.472 44.000 0.00 0.00 36.95 5.14
1428 1621 7.393515 ACAACCATTTCTAGGACAAGTATTTCC 59.606 37.037 0.00 0.00 0.00 3.13
1429 1622 8.336801 ACAACCATTTCTAGGACAAGTATTTC 57.663 34.615 0.00 0.00 0.00 2.17
1430 1623 9.975218 ATACAACCATTTCTAGGACAAGTATTT 57.025 29.630 0.00 0.00 0.00 1.40
1432 1625 8.993424 AGATACAACCATTTCTAGGACAAGTAT 58.007 33.333 0.00 0.00 0.00 2.12
1433 1626 8.375493 AGATACAACCATTTCTAGGACAAGTA 57.625 34.615 0.00 0.00 0.00 2.24
1435 1628 8.696374 TCTAGATACAACCATTTCTAGGACAAG 58.304 37.037 6.10 0.00 38.67 3.16
1436 1629 8.475639 GTCTAGATACAACCATTTCTAGGACAA 58.524 37.037 0.00 0.00 38.67 3.18
1438 1631 8.240267 AGTCTAGATACAACCATTTCTAGGAC 57.760 38.462 0.00 0.00 38.67 3.85
1439 1632 8.840200 AAGTCTAGATACAACCATTTCTAGGA 57.160 34.615 0.00 0.00 38.67 2.94
1491 1684 9.816354 CCGGAAATATTTGTCTTAAAAATGGAT 57.184 29.630 5.17 0.00 0.00 3.41
1492 1685 9.026121 TCCGGAAATATTTGTCTTAAAAATGGA 57.974 29.630 0.00 0.00 0.00 3.41
1493 1686 9.083080 GTCCGGAAATATTTGTCTTAAAAATGG 57.917 33.333 5.23 0.00 0.00 3.16
1494 1687 8.794406 CGTCCGGAAATATTTGTCTTAAAAATG 58.206 33.333 5.23 0.00 0.00 2.32
1495 1688 7.971722 CCGTCCGGAAATATTTGTCTTAAAAAT 59.028 33.333 5.23 0.00 37.50 1.82
1496 1689 7.174599 TCCGTCCGGAAATATTTGTCTTAAAAA 59.825 33.333 5.23 0.00 42.05 1.94
1497 1690 6.654161 TCCGTCCGGAAATATTTGTCTTAAAA 59.346 34.615 5.23 0.00 42.05 1.52
1498 1691 6.171921 TCCGTCCGGAAATATTTGTCTTAAA 58.828 36.000 5.23 0.00 42.05 1.52
1499 1692 5.732633 TCCGTCCGGAAATATTTGTCTTAA 58.267 37.500 5.23 0.00 42.05 1.85
1500 1693 5.341872 TCCGTCCGGAAATATTTGTCTTA 57.658 39.130 5.23 0.00 42.05 2.10
1501 1694 4.189231 CTCCGTCCGGAAATATTTGTCTT 58.811 43.478 5.23 0.00 44.66 3.01
1502 1695 3.431766 CCTCCGTCCGGAAATATTTGTCT 60.432 47.826 5.23 0.00 44.66 3.41
1503 1696 2.870411 CCTCCGTCCGGAAATATTTGTC 59.130 50.000 5.23 0.00 44.66 3.18
1504 1697 2.420967 CCCTCCGTCCGGAAATATTTGT 60.421 50.000 5.23 0.00 44.66 2.83
1505 1698 2.158871 TCCCTCCGTCCGGAAATATTTG 60.159 50.000 5.23 0.00 44.66 2.32
1506 1699 2.104281 CTCCCTCCGTCCGGAAATATTT 59.896 50.000 5.23 0.00 44.66 1.40
1513 1706 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
1515 1708 0.679002 TCAAGTACTCCCTCCGTCCG 60.679 60.000 0.00 0.00 0.00 4.79
1517 1710 4.401837 ACTTAATCAAGTACTCCCTCCGTC 59.598 45.833 0.00 0.00 43.33 4.79
1518 1711 4.351127 ACTTAATCAAGTACTCCCTCCGT 58.649 43.478 0.00 0.00 43.33 4.69
1540 1785 9.920946 AGGGAAACTAGCATTAAATCTAATTGA 57.079 29.630 0.00 0.00 0.00 2.57
1576 1825 7.253422 CACATCTTTTCTGTTCTTTGTTGAGT 58.747 34.615 0.00 0.00 0.00 3.41
1594 1843 2.895404 ACTTTTCCATGCAGCACATCTT 59.105 40.909 0.00 0.00 36.64 2.40
1616 1865 1.613437 CTTTACAAGCTGTTGGGTGGG 59.387 52.381 0.00 0.00 38.07 4.61
1661 1943 0.960364 GAGGGAATCGGCTGTTGCAA 60.960 55.000 0.00 0.00 41.91 4.08
1662 1944 1.377202 GAGGGAATCGGCTGTTGCA 60.377 57.895 0.00 0.00 41.91 4.08
1663 1945 2.115291 GGAGGGAATCGGCTGTTGC 61.115 63.158 0.00 0.00 38.76 4.17
1664 1946 0.322456 TTGGAGGGAATCGGCTGTTG 60.322 55.000 0.00 0.00 0.00 3.33
1665 1947 0.404040 TTTGGAGGGAATCGGCTGTT 59.596 50.000 0.00 0.00 0.00 3.16
1781 2068 5.753716 AGGGATCAAAGGAGAAAAGATGAG 58.246 41.667 0.00 0.00 0.00 2.90
1782 2069 5.786121 AGGGATCAAAGGAGAAAAGATGA 57.214 39.130 0.00 0.00 0.00 2.92
1783 2070 6.127507 GGAAAGGGATCAAAGGAGAAAAGATG 60.128 42.308 0.00 0.00 0.00 2.90
1802 2089 3.457234 AGCAAAAGCGAAAAAGGAAAGG 58.543 40.909 0.00 0.00 0.00 3.11
1815 2102 2.202395 TGTGGGCAGGAGCAAAAGC 61.202 57.895 0.00 0.00 44.61 3.51
1829 2116 1.878953 AGTTTTACTCAGGCGTGTGG 58.121 50.000 12.54 6.93 0.00 4.17
1949 2236 4.858965 AATGAAAAGAGGGAGATGAGCT 57.141 40.909 0.00 0.00 0.00 4.09
1950 2237 4.337836 GGAAATGAAAAGAGGGAGATGAGC 59.662 45.833 0.00 0.00 0.00 4.26
1951 2238 4.886489 GGGAAATGAAAAGAGGGAGATGAG 59.114 45.833 0.00 0.00 0.00 2.90
1952 2239 4.626287 CGGGAAATGAAAAGAGGGAGATGA 60.626 45.833 0.00 0.00 0.00 2.92
1953 2240 3.629398 CGGGAAATGAAAAGAGGGAGATG 59.371 47.826 0.00 0.00 0.00 2.90
1954 2241 3.267031 ACGGGAAATGAAAAGAGGGAGAT 59.733 43.478 0.00 0.00 0.00 2.75
1955 2242 2.642807 ACGGGAAATGAAAAGAGGGAGA 59.357 45.455 0.00 0.00 0.00 3.71
1957 2244 2.790433 CACGGGAAATGAAAAGAGGGA 58.210 47.619 0.00 0.00 0.00 4.20
1958 2245 1.202348 GCACGGGAAATGAAAAGAGGG 59.798 52.381 0.00 0.00 0.00 4.30
1959 2246 1.885887 TGCACGGGAAATGAAAAGAGG 59.114 47.619 0.00 0.00 0.00 3.69
2015 2302 4.348486 AGAGGAGAGATGCTACTGAAACA 58.652 43.478 0.00 0.00 38.15 2.83
2034 2321 5.633830 TGCCAAAGCATAGAAAGAAAGAG 57.366 39.130 0.00 0.00 46.52 2.85
2053 2340 4.948847 AGGAACAGAAAAAGATGTTTGCC 58.051 39.130 0.00 0.00 39.66 4.52
2058 2345 7.260603 CAGTGAAAAGGAACAGAAAAAGATGT 58.739 34.615 0.00 0.00 0.00 3.06
2059 2346 6.698766 CCAGTGAAAAGGAACAGAAAAAGATG 59.301 38.462 0.00 0.00 0.00 2.90
2100 2390 1.081242 CCCGACTGTGCAATGCAAC 60.081 57.895 10.44 5.14 41.47 4.17
2118 2408 2.675767 TAACGGATCGATACGACAGC 57.324 50.000 35.47 3.00 39.18 4.40
2157 2447 4.276431 GCACTACTCTACCAGTTAGCTAGG 59.724 50.000 0.00 0.00 36.43 3.02
2190 2480 3.771577 TGTGAAAGAAGAGGAAGGTCC 57.228 47.619 0.00 0.00 36.58 4.46
2195 2487 4.040461 AGAACGGATGTGAAAGAAGAGGAA 59.960 41.667 0.00 0.00 0.00 3.36
2197 2489 3.931578 AGAACGGATGTGAAAGAAGAGG 58.068 45.455 0.00 0.00 0.00 3.69
2281 2573 1.474332 AAAACCCATGCTGCACCCTG 61.474 55.000 3.57 0.00 0.00 4.45
2282 2574 1.152269 AAAACCCATGCTGCACCCT 60.152 52.632 3.57 0.00 0.00 4.34
2283 2575 1.293179 GAAAACCCATGCTGCACCC 59.707 57.895 3.57 0.00 0.00 4.61
2306 2598 2.834549 TCTCTCGGGCAGAAGAATCTTT 59.165 45.455 0.00 0.00 32.03 2.52
2340 2632 1.179814 AGAGTTCCAGCGTCGGTCTT 61.180 55.000 0.00 0.00 0.00 3.01
2341 2633 1.604023 AGAGTTCCAGCGTCGGTCT 60.604 57.895 0.00 0.00 0.00 3.85
2343 2635 2.651361 CAGAGTTCCAGCGTCGGT 59.349 61.111 0.00 0.00 0.00 4.69
2344 2636 2.811317 GCAGAGTTCCAGCGTCGG 60.811 66.667 0.00 0.00 0.00 4.79
2526 2818 0.376152 CGCAAGTCCATGATGCTCAC 59.624 55.000 0.00 0.00 37.92 3.51
2574 2866 8.017587 ACTAAAAAGACAAACAAACAAGCAAG 57.982 30.769 0.00 0.00 0.00 4.01
2591 2883 6.213802 ACCCCCTCTCTTCTCTAACTAAAAAG 59.786 42.308 0.00 0.00 0.00 2.27
2593 2885 5.662597 ACCCCCTCTCTTCTCTAACTAAAA 58.337 41.667 0.00 0.00 0.00 1.52
2615 2907 5.515184 AGCACAAAAACACCAAAACAAAAC 58.485 33.333 0.00 0.00 0.00 2.43
2647 2939 6.072119 ACAGGCTTATTCCGGTTAAAAAGAAG 60.072 38.462 0.00 1.83 30.25 2.85
2671 2963 5.230726 GCACAGCTATTCATTGCAAATGTAC 59.769 40.000 1.71 0.00 33.24 2.90
2674 2966 3.242016 CGCACAGCTATTCATTGCAAATG 59.758 43.478 1.71 2.77 32.51 2.32
2675 2967 3.119388 ACGCACAGCTATTCATTGCAAAT 60.119 39.130 1.71 0.00 32.51 2.32
2676 2968 2.228582 ACGCACAGCTATTCATTGCAAA 59.771 40.909 1.71 0.00 32.51 3.68
2678 2970 1.398041 GACGCACAGCTATTCATTGCA 59.602 47.619 0.00 0.00 32.51 4.08
2679 2971 1.398041 TGACGCACAGCTATTCATTGC 59.602 47.619 0.00 0.00 0.00 3.56
2681 2973 3.599343 TCTTGACGCACAGCTATTCATT 58.401 40.909 0.00 0.00 0.00 2.57
2682 2974 3.193263 CTCTTGACGCACAGCTATTCAT 58.807 45.455 0.00 0.00 0.00 2.57
2685 2977 1.338105 TGCTCTTGACGCACAGCTATT 60.338 47.619 0.00 0.00 31.40 1.73
2688 2980 0.604780 ATTGCTCTTGACGCACAGCT 60.605 50.000 9.72 0.00 37.07 4.24
2690 2982 0.167470 CCATTGCTCTTGACGCACAG 59.833 55.000 0.00 0.00 37.07 3.66
2691 2983 0.250252 TCCATTGCTCTTGACGCACA 60.250 50.000 0.00 0.00 37.07 4.57
2693 2985 1.372582 GATCCATTGCTCTTGACGCA 58.627 50.000 0.00 0.00 35.22 5.24
2694 2986 0.302890 CGATCCATTGCTCTTGACGC 59.697 55.000 0.00 0.00 0.00 5.19
2695 2987 0.933097 CCGATCCATTGCTCTTGACG 59.067 55.000 0.00 0.00 0.00 4.35
2806 3263 3.857052 AGACTTGCGTATTCATTTCGGA 58.143 40.909 0.00 0.00 0.00 4.55
2830 3287 7.844009 ACCTTACCGTGTTCAGAAAGATATAA 58.156 34.615 0.00 0.00 0.00 0.98
2836 3293 3.991367 AGACCTTACCGTGTTCAGAAAG 58.009 45.455 0.00 0.00 0.00 2.62
2840 3301 6.796705 AAATTAAGACCTTACCGTGTTCAG 57.203 37.500 0.00 0.00 0.00 3.02
2862 3323 9.691362 GTTTCTTGATCTAATGCCTTACAAAAA 57.309 29.630 0.00 0.00 0.00 1.94
2863 3324 8.020819 CGTTTCTTGATCTAATGCCTTACAAAA 58.979 33.333 0.00 0.00 0.00 2.44
2894 3355 7.464358 CACCGGTAAACTTTCTTGATCTAATG 58.536 38.462 6.87 0.00 0.00 1.90
2897 3358 4.933400 GCACCGGTAAACTTTCTTGATCTA 59.067 41.667 6.87 0.00 0.00 1.98
2899 3360 3.751698 AGCACCGGTAAACTTTCTTGATC 59.248 43.478 6.87 0.00 0.00 2.92
2900 3361 3.751518 AGCACCGGTAAACTTTCTTGAT 58.248 40.909 6.87 0.00 0.00 2.57
2901 3362 3.202829 AGCACCGGTAAACTTTCTTGA 57.797 42.857 6.87 0.00 0.00 3.02
2902 3363 3.982576 AAGCACCGGTAAACTTTCTTG 57.017 42.857 6.87 0.00 0.00 3.02
2962 3440 6.018180 GGAAACATCTTAGAGAAACACGTGTT 60.018 38.462 27.70 27.70 40.50 3.32
2963 3441 5.465724 GGAAACATCTTAGAGAAACACGTGT 59.534 40.000 17.22 17.22 0.00 4.49
2964 3442 5.465390 TGGAAACATCTTAGAGAAACACGTG 59.535 40.000 15.48 15.48 33.40 4.49
2965 3443 5.607477 TGGAAACATCTTAGAGAAACACGT 58.393 37.500 0.00 0.00 33.40 4.49
3045 3528 0.682209 GGACTCCAGCACCTACGGTA 60.682 60.000 0.00 0.00 32.11 4.02
3046 3529 1.982938 GGACTCCAGCACCTACGGT 60.983 63.158 0.00 0.00 35.62 4.83
3047 3530 2.893398 GGACTCCAGCACCTACGG 59.107 66.667 0.00 0.00 0.00 4.02
3048 3531 2.490217 CGGACTCCAGCACCTACG 59.510 66.667 0.00 0.00 0.00 3.51
3049 3532 2.184579 GCGGACTCCAGCACCTAC 59.815 66.667 6.94 0.00 0.00 3.18
3076 3560 7.361286 GCCAAACAGATACTCTAGAAAAGTTGG 60.361 40.741 0.00 0.00 0.00 3.77
3083 3567 5.401531 AACGCCAAACAGATACTCTAGAA 57.598 39.130 0.00 0.00 0.00 2.10
3085 3569 5.168569 TGAAACGCCAAACAGATACTCTAG 58.831 41.667 0.00 0.00 0.00 2.43
3086 3570 5.142061 TGAAACGCCAAACAGATACTCTA 57.858 39.130 0.00 0.00 0.00 2.43
3087 3571 4.002906 TGAAACGCCAAACAGATACTCT 57.997 40.909 0.00 0.00 0.00 3.24
3088 3572 4.391830 TCATGAAACGCCAAACAGATACTC 59.608 41.667 0.00 0.00 0.00 2.59
3089 3573 4.323417 TCATGAAACGCCAAACAGATACT 58.677 39.130 0.00 0.00 0.00 2.12
3092 3576 3.758023 TCATCATGAAACGCCAAACAGAT 59.242 39.130 0.00 0.00 0.00 2.90
3108 3592 0.749454 GCGGACAAGGGCTTCATCAT 60.749 55.000 0.00 0.00 0.00 2.45
3112 3596 2.281484 GTGCGGACAAGGGCTTCA 60.281 61.111 0.63 0.00 0.00 3.02
3114 3598 4.250305 ACGTGCGGACAAGGGCTT 62.250 61.111 8.11 0.00 0.00 4.35
3115 3599 4.681978 GACGTGCGGACAAGGGCT 62.682 66.667 8.11 0.00 0.00 5.19
3121 3605 4.409218 GTAGCGGACGTGCGGACA 62.409 66.667 30.42 3.68 40.67 4.02
3128 3633 3.507009 GAGCGAGGTAGCGGACGT 61.507 66.667 0.00 0.00 43.00 4.34
3129 3634 4.253257 GGAGCGAGGTAGCGGACG 62.253 72.222 0.00 5.24 43.00 4.79
3131 3636 3.138798 GTGGAGCGAGGTAGCGGA 61.139 66.667 0.00 0.00 43.00 5.54
3137 3642 1.384989 CCATCTACGTGGAGCGAGGT 61.385 60.000 7.91 0.00 44.77 3.85
3242 3760 1.014352 GGCACAGTTTATAGGCCGTG 58.986 55.000 0.00 0.00 34.56 4.94
3243 3761 0.107361 GGGCACAGTTTATAGGCCGT 60.107 55.000 0.00 0.00 45.52 5.68
3263 3782 4.655762 TGATGTATTGTTCCGAGAGAGG 57.344 45.455 0.00 0.00 0.00 3.69
3337 3876 2.439156 GCAGGCAAGGAATCGGCT 60.439 61.111 0.00 0.00 38.82 5.52
3338 3877 2.439156 AGCAGGCAAGGAATCGGC 60.439 61.111 0.00 0.00 0.00 5.54
3339 3878 2.768492 GCAGCAGGCAAGGAATCGG 61.768 63.158 0.00 0.00 43.97 4.18
3340 3879 2.796651 GCAGCAGGCAAGGAATCG 59.203 61.111 0.00 0.00 43.97 3.34
3354 3893 1.134461 AGGAAGCTACAGATGCTGCAG 60.134 52.381 10.11 10.11 41.03 4.41
3377 3939 0.532862 CCATTAATCAGCCGCGGACT 60.533 55.000 33.48 22.91 0.00 3.85


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

AutoCloner maintained by Alex Coulton.