Multiple sequence alignment - TraesCS6A01G188000

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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 TraesCS6A01G188000 chr6A 100.000 3586 0 0 1 3586 227543700 227540115 0.000000e+00 6623.0
1 TraesCS6A01G188000 chr6A 94.331 1464 82 1 2 1465 14539070 14537608 0.000000e+00 2242.0
2 TraesCS6A01G188000 chr6A 94.944 890 42 3 1804 2691 14537566 14536678 0.000000e+00 1391.0
3 TraesCS6A01G188000 chr6A 97.788 226 5 0 1241 1466 227542234 227542009 1.210000e-104 390.0
4 TraesCS6A01G188000 chr3B 91.729 1995 158 7 1475 3464 57838794 57836802 0.000000e+00 2763.0
5 TraesCS6A01G188000 chr3B 91.120 1464 88 12 2 1465 172068743 172070164 0.000000e+00 1945.0
6 TraesCS6A01G188000 chr3B 90.710 1464 93 9 2 1465 172188779 172190199 0.000000e+00 1910.0
7 TraesCS6A01G188000 chr3B 92.500 1040 75 3 1474 2513 442045963 442046999 0.000000e+00 1485.0
8 TraesCS6A01G188000 chr3B 92.404 1040 74 4 1474 2513 697443205 697442171 0.000000e+00 1478.0
9 TraesCS6A01G188000 chr3B 93.503 985 62 1 1474 2458 790214344 790215326 0.000000e+00 1463.0
10 TraesCS6A01G188000 chr3B 92.487 985 71 2 1474 2458 459972552 459971571 0.000000e+00 1406.0
11 TraesCS6A01G188000 chr3B 92.165 702 36 5 2 703 57839713 57839031 0.000000e+00 974.0
12 TraesCS6A01G188000 chr3B 89.036 757 61 3 709 1465 790213827 790214561 0.000000e+00 918.0
13 TraesCS6A01G188000 chr7B 91.254 2001 156 10 1475 3469 328124871 328126858 0.000000e+00 2708.0
14 TraesCS6A01G188000 chr7B 90.984 1464 91 7 2 1465 328123665 328125087 0.000000e+00 1934.0
15 TraesCS6A01G188000 chr7B 92.487 985 72 1 1474 2458 455330688 455329706 0.000000e+00 1408.0
16 TraesCS6A01G188000 chr6D 90.177 1639 120 22 1837 3469 199472456 199470853 0.000000e+00 2097.0
17 TraesCS6A01G188000 chr6D 92.323 990 68 6 2055 3039 246424217 246423231 0.000000e+00 1400.0
18 TraesCS6A01G188000 chr6D 87.517 729 77 9 741 1465 246425227 246424509 0.000000e+00 830.0
19 TraesCS6A01G188000 chr1B 90.851 1552 121 7 1923 3469 395142875 395144410 0.000000e+00 2060.0
20 TraesCS6A01G188000 chr1B 90.219 777 56 11 2060 2834 490599530 490600288 0.000000e+00 996.0
21 TraesCS6A01G188000 chr4D 89.848 1320 96 18 2158 3469 486192106 486190817 0.000000e+00 1661.0
22 TraesCS6A01G188000 chr4D 86.813 728 86 9 741 1465 486210057 486209337 0.000000e+00 804.0
23 TraesCS6A01G188000 chr6B 89.959 1215 89 12 1623 2834 81735565 81736749 0.000000e+00 1537.0
24 TraesCS6A01G188000 chr6B 93.175 967 63 1 1547 2513 527591232 527590269 0.000000e+00 1417.0
25 TraesCS6A01G188000 chr6B 90.208 674 64 1 725 1398 41242462 41243133 0.000000e+00 878.0
26 TraesCS6A01G188000 chr6B 88.966 580 62 2 2886 3465 64114186 64113609 0.000000e+00 715.0
27 TraesCS6A01G188000 chr6B 88.514 592 65 3 2879 3469 81736744 81737333 0.000000e+00 713.0
28 TraesCS6A01G188000 chr6B 92.099 443 32 3 282 724 41232475 41232914 3.930000e-174 621.0
29 TraesCS6A01G188000 chr6B 94.286 105 5 1 281 385 11946260 11946363 3.710000e-35 159.0
30 TraesCS6A01G188000 chr7A 92.603 1041 74 3 1474 2513 375177741 375178779 0.000000e+00 1493.0
31 TraesCS6A01G188000 chr7A 89.879 1077 74 9 389 1465 375176917 375177958 0.000000e+00 1352.0
32 TraesCS6A01G188000 chr1D 88.756 1085 88 12 2389 3469 429417120 429416066 0.000000e+00 1297.0
33 TraesCS6A01G188000 chr1D 91.704 904 74 1 560 1463 429425258 429424356 0.000000e+00 1253.0
34 TraesCS6A01G188000 chr1D 95.737 563 24 0 2 564 429425939 429425377 0.000000e+00 907.0
35 TraesCS6A01G188000 chr5D 86.349 945 105 18 2539 3472 397471191 397470260 0.000000e+00 1009.0
36 TraesCS6A01G188000 chr5B 94.937 632 24 2 2 633 385244708 385245331 0.000000e+00 983.0
37 TraesCS6A01G188000 chrUn 89.911 674 66 1 725 1398 337811188 337810517 0.000000e+00 867.0
38 TraesCS6A01G188000 chr2B 88.027 593 68 2 2879 3469 436007607 436007016 0.000000e+00 699.0
39 TraesCS6A01G188000 chr3D 90.000 350 28 2 495 837 526460121 526460470 2.540000e-121 446.0
40 TraesCS6A01G188000 chr3D 97.674 43 0 1 3 45 613783758 613783799 4.970000e-09 73.1
41 TraesCS6A01G188000 chr2A 86.322 329 32 7 2685 3007 656184478 656184799 2.650000e-91 346.0
42 TraesCS6A01G188000 chr2A 85.976 328 36 5 2685 3007 71486215 71485893 3.430000e-90 342.0
43 TraesCS6A01G188000 chr4A 85.152 330 34 10 2685 3007 31213825 31213504 1.240000e-84 324.0


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 TraesCS6A01G188000 chr6A 227540115 227543700 3585 True 3506.5 6623 98.8940 1 3586 2 chr6A.!!$R2 3585
1 TraesCS6A01G188000 chr6A 14536678 14539070 2392 True 1816.5 2242 94.6375 2 2691 2 chr6A.!!$R1 2689
2 TraesCS6A01G188000 chr3B 172068743 172070164 1421 False 1945.0 1945 91.1200 2 1465 1 chr3B.!!$F1 1463
3 TraesCS6A01G188000 chr3B 172188779 172190199 1420 False 1910.0 1910 90.7100 2 1465 1 chr3B.!!$F2 1463
4 TraesCS6A01G188000 chr3B 57836802 57839713 2911 True 1868.5 2763 91.9470 2 3464 2 chr3B.!!$R3 3462
5 TraesCS6A01G188000 chr3B 442045963 442046999 1036 False 1485.0 1485 92.5000 1474 2513 1 chr3B.!!$F3 1039
6 TraesCS6A01G188000 chr3B 697442171 697443205 1034 True 1478.0 1478 92.4040 1474 2513 1 chr3B.!!$R2 1039
7 TraesCS6A01G188000 chr3B 459971571 459972552 981 True 1406.0 1406 92.4870 1474 2458 1 chr3B.!!$R1 984
8 TraesCS6A01G188000 chr3B 790213827 790215326 1499 False 1190.5 1463 91.2695 709 2458 2 chr3B.!!$F4 1749
9 TraesCS6A01G188000 chr7B 328123665 328126858 3193 False 2321.0 2708 91.1190 2 3469 2 chr7B.!!$F1 3467
10 TraesCS6A01G188000 chr7B 455329706 455330688 982 True 1408.0 1408 92.4870 1474 2458 1 chr7B.!!$R1 984
11 TraesCS6A01G188000 chr6D 199470853 199472456 1603 True 2097.0 2097 90.1770 1837 3469 1 chr6D.!!$R1 1632
12 TraesCS6A01G188000 chr6D 246423231 246425227 1996 True 1115.0 1400 89.9200 741 3039 2 chr6D.!!$R2 2298
13 TraesCS6A01G188000 chr1B 395142875 395144410 1535 False 2060.0 2060 90.8510 1923 3469 1 chr1B.!!$F1 1546
14 TraesCS6A01G188000 chr1B 490599530 490600288 758 False 996.0 996 90.2190 2060 2834 1 chr1B.!!$F2 774
15 TraesCS6A01G188000 chr4D 486190817 486192106 1289 True 1661.0 1661 89.8480 2158 3469 1 chr4D.!!$R1 1311
16 TraesCS6A01G188000 chr4D 486209337 486210057 720 True 804.0 804 86.8130 741 1465 1 chr4D.!!$R2 724
17 TraesCS6A01G188000 chr6B 527590269 527591232 963 True 1417.0 1417 93.1750 1547 2513 1 chr6B.!!$R2 966
18 TraesCS6A01G188000 chr6B 81735565 81737333 1768 False 1125.0 1537 89.2365 1623 3469 2 chr6B.!!$F4 1846
19 TraesCS6A01G188000 chr6B 41242462 41243133 671 False 878.0 878 90.2080 725 1398 1 chr6B.!!$F3 673
20 TraesCS6A01G188000 chr6B 64113609 64114186 577 True 715.0 715 88.9660 2886 3465 1 chr6B.!!$R1 579
21 TraesCS6A01G188000 chr7A 375176917 375178779 1862 False 1422.5 1493 91.2410 389 2513 2 chr7A.!!$F1 2124
22 TraesCS6A01G188000 chr1D 429416066 429417120 1054 True 1297.0 1297 88.7560 2389 3469 1 chr1D.!!$R1 1080
23 TraesCS6A01G188000 chr1D 429424356 429425939 1583 True 1080.0 1253 93.7205 2 1463 2 chr1D.!!$R2 1461
24 TraesCS6A01G188000 chr5D 397470260 397471191 931 True 1009.0 1009 86.3490 2539 3472 1 chr5D.!!$R1 933
25 TraesCS6A01G188000 chr5B 385244708 385245331 623 False 983.0 983 94.9370 2 633 1 chr5B.!!$F1 631
26 TraesCS6A01G188000 chrUn 337810517 337811188 671 True 867.0 867 89.9110 725 1398 1 chrUn.!!$R1 673
27 TraesCS6A01G188000 chr2B 436007016 436007607 591 True 699.0 699 88.0270 2879 3469 1 chr2B.!!$R1 590

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
500 507 0.617413 CTTGACTGCTCAGGGTGGAT 59.383 55.0 1.66 0.0 0.0 3.41 F
1122 1260 0.034574 TGTTGCTTCTGTGGTGTGGT 60.035 50.0 0.00 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1460 1598 0.037160 GGGGGACAAAGCGGTAGAAA 59.963 55.000 0.0 0.0 0.0 2.52 R
3070 3247 1.272203 ACCATACCCAACAATTCGGCA 60.272 47.619 0.0 0.0 0.0 5.69 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
49 50 4.883585 TGTGATGATGAGTCCATTTTAGCC 59.116 41.667 0.00 0.00 32.09 3.93
63 64 7.220108 GTCCATTTTAGCCGAAATAATGTTGTC 59.780 37.037 0.00 0.00 0.00 3.18
78 79 1.993370 GTTGTCGATAGTGACCACAGC 59.007 52.381 2.78 0.00 38.11 4.40
90 91 2.156098 GACCACAGCGGGATTTTAACA 58.844 47.619 0.00 0.00 40.22 2.41
290 297 3.806380 GATGACTGCATCTGATTGACCT 58.194 45.455 0.00 0.00 45.93 3.85
291 298 4.953667 GATGACTGCATCTGATTGACCTA 58.046 43.478 0.00 0.00 45.93 3.08
337 344 5.228220 CGTACTATCGCTTTCTCAAGTCAAG 59.772 44.000 0.00 0.00 31.86 3.02
355 362 4.682860 GTCAAGTCAAGCAACAATTCATGG 59.317 41.667 0.00 0.00 0.00 3.66
361 368 0.896923 GCAACAATTCATGGGGCTCA 59.103 50.000 0.00 0.00 31.70 4.26
500 507 0.617413 CTTGACTGCTCAGGGTGGAT 59.383 55.000 1.66 0.00 0.00 3.41
593 723 5.357878 TGTTCAAGAAGTTTCATGAGTTGCT 59.642 36.000 0.00 0.00 36.43 3.91
633 765 8.783093 TCTAGTTTCATTGATGGTGTTTAACAG 58.217 33.333 0.00 0.00 0.00 3.16
651 783 2.238898 ACAGTACTTGCCCTTGTATCCC 59.761 50.000 0.00 0.00 0.00 3.85
664 796 5.934625 CCCTTGTATCCCTTATTCAATCTCG 59.065 44.000 0.00 0.00 0.00 4.04
838 970 9.961265 AACTTTCTTTAACATAGTAACAAAGGC 57.039 29.630 0.00 0.00 0.00 4.35
860 992 3.241530 TCCCACGCTGGCAACTCT 61.242 61.111 0.00 0.00 35.79 3.24
972 1110 2.753452 TCGGTTTGGTTTGCTGTTGTTA 59.247 40.909 0.00 0.00 0.00 2.41
1042 1180 3.785122 GACCCCAACAAGCCCACGT 62.785 63.158 0.00 0.00 0.00 4.49
1044 1182 2.518349 CCCAACAAGCCCACGTGT 60.518 61.111 15.65 0.00 40.44 4.49
1058 1196 2.668550 GTGTCCCCGAGCGCTTTT 60.669 61.111 13.26 0.00 0.00 2.27
1090 1228 0.112606 TGAGTCCCAGTCTCGGTTCT 59.887 55.000 0.00 0.00 34.99 3.01
1122 1260 0.034574 TGTTGCTTCTGTGGTGTGGT 60.035 50.000 0.00 0.00 0.00 4.16
1130 1268 2.027897 GTGGTGTGGTGTCGCGTA 59.972 61.111 5.77 0.00 0.00 4.42
1150 1288 0.321564 CTGACCGAGGATTTGGTGCA 60.322 55.000 0.00 0.00 41.42 4.57
1197 1335 4.689062 TCAGGAAGGAGTACAAGGAGAAT 58.311 43.478 0.00 0.00 0.00 2.40
1207 1345 0.613260 CAAGGAGAATCACCCCGACA 59.387 55.000 0.00 0.00 36.25 4.35
1290 1428 0.736053 TGTTCGTTCAAACTGGTGGC 59.264 50.000 0.00 0.00 0.00 5.01
1292 1430 0.745128 TTCGTTCAAACTGGTGGCGT 60.745 50.000 0.00 0.00 0.00 5.68
1319 1457 5.232414 CGAGATGAGTTTCCTCGTTAATTCC 59.768 44.000 0.00 0.00 43.20 3.01
1339 1477 3.131396 CCGTGTCCTGATATGGTTTAGC 58.869 50.000 0.00 0.00 0.00 3.09
1351 1489 8.815565 TGATATGGTTTAGCTTGGTTGAATTA 57.184 30.769 0.00 0.00 0.00 1.40
1357 1495 7.094377 TGGTTTAGCTTGGTTGAATTACAGATC 60.094 37.037 0.00 0.00 0.00 2.75
1400 1538 3.106827 TGGAAGTCCATGAGTGATGCTA 58.893 45.455 0.00 0.00 42.01 3.49
1441 1579 1.482593 CCCTCTCTGTTACCGCTCAAT 59.517 52.381 0.00 0.00 0.00 2.57
1442 1580 2.093447 CCCTCTCTGTTACCGCTCAATT 60.093 50.000 0.00 0.00 0.00 2.32
1443 1581 2.932614 CCTCTCTGTTACCGCTCAATTG 59.067 50.000 0.00 0.00 0.00 2.32
1444 1582 2.932614 CTCTCTGTTACCGCTCAATTGG 59.067 50.000 5.42 0.00 0.00 3.16
1445 1583 2.009774 CTCTGTTACCGCTCAATTGGG 58.990 52.381 5.42 2.47 0.00 4.12
1446 1584 1.349688 TCTGTTACCGCTCAATTGGGT 59.650 47.619 7.27 8.54 37.84 4.51
1447 1585 1.468520 CTGTTACCGCTCAATTGGGTG 59.531 52.381 12.12 12.12 35.28 4.61
1448 1586 1.202830 TGTTACCGCTCAATTGGGTGT 60.203 47.619 17.37 12.10 35.28 4.16
1449 1587 1.883926 GTTACCGCTCAATTGGGTGTT 59.116 47.619 17.37 6.12 35.28 3.32
1450 1588 1.529226 TACCGCTCAATTGGGTGTTG 58.471 50.000 17.37 5.91 35.28 3.33
1451 1589 1.178534 ACCGCTCAATTGGGTGTTGG 61.179 55.000 17.37 11.39 31.52 3.77
1452 1590 1.178534 CCGCTCAATTGGGTGTTGGT 61.179 55.000 17.37 0.00 0.00 3.67
1453 1591 0.673437 CGCTCAATTGGGTGTTGGTT 59.327 50.000 10.86 0.00 0.00 3.67
1454 1592 1.068434 CGCTCAATTGGGTGTTGGTTT 59.932 47.619 10.86 0.00 0.00 3.27
1455 1593 2.294791 CGCTCAATTGGGTGTTGGTTTA 59.705 45.455 10.86 0.00 0.00 2.01
1456 1594 3.649073 GCTCAATTGGGTGTTGGTTTAC 58.351 45.455 7.27 0.00 0.00 2.01
1457 1595 3.320826 GCTCAATTGGGTGTTGGTTTACT 59.679 43.478 7.27 0.00 0.00 2.24
1458 1596 4.558697 GCTCAATTGGGTGTTGGTTTACTC 60.559 45.833 7.27 0.00 0.00 2.59
1459 1597 3.566322 TCAATTGGGTGTTGGTTTACTCG 59.434 43.478 5.42 0.00 0.00 4.18
1460 1598 2.713863 TTGGGTGTTGGTTTACTCGT 57.286 45.000 0.00 0.00 0.00 4.18
1461 1599 2.713863 TGGGTGTTGGTTTACTCGTT 57.286 45.000 0.00 0.00 0.00 3.85
1462 1600 3.002038 TGGGTGTTGGTTTACTCGTTT 57.998 42.857 0.00 0.00 0.00 3.60
1463 1601 2.944349 TGGGTGTTGGTTTACTCGTTTC 59.056 45.455 0.00 0.00 0.00 2.78
1464 1602 3.208594 GGGTGTTGGTTTACTCGTTTCT 58.791 45.455 0.00 0.00 0.00 2.52
1465 1603 4.141756 TGGGTGTTGGTTTACTCGTTTCTA 60.142 41.667 0.00 0.00 0.00 2.10
1466 1604 4.212004 GGGTGTTGGTTTACTCGTTTCTAC 59.788 45.833 0.00 0.00 0.00 2.59
1467 1605 4.212004 GGTGTTGGTTTACTCGTTTCTACC 59.788 45.833 0.00 0.00 0.00 3.18
1468 1606 4.050553 TGTTGGTTTACTCGTTTCTACCG 58.949 43.478 0.00 0.00 0.00 4.02
1469 1607 2.676076 TGGTTTACTCGTTTCTACCGC 58.324 47.619 0.00 0.00 0.00 5.68
1470 1608 2.297033 TGGTTTACTCGTTTCTACCGCT 59.703 45.455 0.00 0.00 0.00 5.52
1471 1609 3.243839 TGGTTTACTCGTTTCTACCGCTT 60.244 43.478 0.00 0.00 0.00 4.68
1472 1610 3.742882 GGTTTACTCGTTTCTACCGCTTT 59.257 43.478 0.00 0.00 0.00 3.51
1506 1646 2.543031 CCTCTGTCTCGTTGTTCGTTCA 60.543 50.000 0.00 0.00 40.80 3.18
1516 1656 0.736053 TGTTCGTTCAAACTGGTGGC 59.264 50.000 0.00 0.00 0.00 5.01
1536 1676 1.285578 GCTGCGAGATGAGTTTCCTC 58.714 55.000 0.00 0.00 38.27 3.71
1565 1705 3.131396 CCGTGTCCTGATATGGTTTAGC 58.869 50.000 0.00 0.00 0.00 3.09
1577 1717 8.815565 TGATATGGTTTAGCTTGGTTGAATTA 57.184 30.769 0.00 0.00 0.00 1.40
1583 1723 7.094377 TGGTTTAGCTTGGTTGAATTACAGATC 60.094 37.037 0.00 0.00 0.00 2.75
1626 1766 3.106827 TGGAAGTCCATGAGTGATGCTA 58.893 45.455 0.00 0.00 42.01 3.49
1669 1809 2.932614 CCTCTCTGTTACCGCTCAATTG 59.067 50.000 0.00 0.00 0.00 2.32
1684 1824 4.083271 GCTCAATTGGGTGTCAGTTTACTC 60.083 45.833 7.27 0.00 0.00 2.59
1691 1831 4.341806 TGGGTGTCAGTTTACTCGTTTCTA 59.658 41.667 0.00 0.00 0.00 2.10
1824 1964 0.677731 TCCAATGGCAGTAGCAGCAC 60.678 55.000 0.00 0.00 44.61 4.40
2013 2157 7.516198 ACTAGCTGAATTTCTGTTGTCATTT 57.484 32.000 0.00 0.00 0.00 2.32
2136 2281 4.961511 GCACACGTCTGGCACCGA 62.962 66.667 8.62 0.00 0.00 4.69
2258 2404 1.451067 CTCCTGCTTTTCTGCTCCTG 58.549 55.000 0.00 0.00 0.00 3.86
2604 2760 4.080975 TGTGAGTAGATGTTGATGATGCCA 60.081 41.667 0.00 0.00 0.00 4.92
2673 2830 5.195503 CATGCATATACGTACATGTCAGC 57.804 43.478 14.90 1.65 36.11 4.26
2766 2933 5.585047 GTGTTATGTAAACCTGGGAGATGTC 59.415 44.000 0.00 0.00 0.00 3.06
2787 2954 7.662604 TGTCTTATGTGATGTGATATGATGC 57.337 36.000 0.00 0.00 0.00 3.91
2795 2962 7.590279 TGTGATGTGATATGATGCATGATTTC 58.410 34.615 2.46 6.80 0.00 2.17
2850 3018 1.277842 ACAAGGTCGGATGCATGTGTA 59.722 47.619 2.46 0.00 0.00 2.90
2856 3024 4.587262 AGGTCGGATGCATGTGTATAACTA 59.413 41.667 2.46 0.00 0.00 2.24
2881 3049 1.986882 AAGAGGTCTTGTGCCCAAAG 58.013 50.000 0.00 0.00 34.38 2.77
2888 3056 4.058124 GGTCTTGTGCCCAAAGAATTTTC 58.942 43.478 0.00 0.00 35.03 2.29
3070 3247 9.462606 CCTAGTATGGAAGAACCTAACAAAAAT 57.537 33.333 0.00 0.00 39.86 1.82
3090 3267 1.272203 TGCCGAATTGTTGGGTATGGT 60.272 47.619 0.00 0.00 0.00 3.55
3094 3271 2.422127 CGAATTGTTGGGTATGGTCCAC 59.578 50.000 0.00 0.00 33.43 4.02
3113 3291 4.879545 TCCACGCTGAAATTAATAGGGAAC 59.120 41.667 7.55 0.00 0.00 3.62
3141 3324 0.112995 AGGCTGAATTGTTGGGCTCA 59.887 50.000 0.00 0.00 0.00 4.26
3193 3376 4.451096 GCTGAATCTTGTCAACGACCTTTA 59.549 41.667 0.00 0.00 0.00 1.85
3231 3414 2.203015 ACGTCAGCTTGCCACGTT 60.203 55.556 12.62 1.24 44.10 3.99
3234 3417 0.944311 CGTCAGCTTGCCACGTTAGT 60.944 55.000 6.55 0.00 0.00 2.24
3241 3424 0.390124 TTGCCACGTTAGTTCCGACT 59.610 50.000 0.00 0.00 39.97 4.18
3245 3428 1.269936 CCACGTTAGTTCCGACTTGGT 60.270 52.381 0.00 0.00 39.52 3.67
3246 3429 1.790623 CACGTTAGTTCCGACTTGGTG 59.209 52.381 0.00 0.00 39.52 4.17
3334 3517 1.699730 TCCACGACCTTCTCACAGAA 58.300 50.000 0.00 0.00 32.50 3.02
3465 3649 5.790495 GTCGCAAGTTGACATATTTCTTGTC 59.210 40.000 7.16 0.00 40.51 3.18
3469 3653 5.862924 AGTTGACATATTTCTTGTCGTGG 57.137 39.130 0.00 0.00 45.14 4.94
3472 3656 4.260985 TGACATATTTCTTGTCGTGGCAT 58.739 39.130 0.00 0.00 45.14 4.40
3473 3657 4.094739 TGACATATTTCTTGTCGTGGCATG 59.905 41.667 0.00 0.00 45.14 4.06
3474 3658 3.181497 ACATATTTCTTGTCGTGGCATGC 60.181 43.478 9.90 9.90 0.00 4.06
3475 3659 0.527565 ATTTCTTGTCGTGGCATGCC 59.472 50.000 30.54 30.54 0.00 4.40
3476 3660 1.851021 TTTCTTGTCGTGGCATGCCG 61.851 55.000 30.87 20.13 39.42 5.69
3477 3661 3.049674 CTTGTCGTGGCATGCCGT 61.050 61.111 30.87 0.00 39.42 5.68
3478 3662 1.739929 CTTGTCGTGGCATGCCGTA 60.740 57.895 30.87 16.31 39.42 4.02
3479 3663 1.295357 CTTGTCGTGGCATGCCGTAA 61.295 55.000 30.87 18.65 39.42 3.18
3480 3664 1.295357 TTGTCGTGGCATGCCGTAAG 61.295 55.000 30.87 20.75 39.42 2.34
3481 3665 1.740296 GTCGTGGCATGCCGTAAGT 60.740 57.895 30.87 0.00 39.42 2.24
3482 3666 1.004320 TCGTGGCATGCCGTAAGTT 60.004 52.632 30.87 0.00 39.42 2.66
3483 3667 0.604243 TCGTGGCATGCCGTAAGTTT 60.604 50.000 30.87 0.00 39.42 2.66
3484 3668 1.080298 CGTGGCATGCCGTAAGTTTA 58.920 50.000 30.87 8.74 39.42 2.01
3485 3669 1.465387 CGTGGCATGCCGTAAGTTTAA 59.535 47.619 30.87 7.94 39.42 1.52
3486 3670 2.096819 CGTGGCATGCCGTAAGTTTAAT 59.903 45.455 30.87 0.00 39.42 1.40
3487 3671 3.434637 GTGGCATGCCGTAAGTTTAATG 58.565 45.455 30.87 0.00 39.42 1.90
3488 3672 3.085533 TGGCATGCCGTAAGTTTAATGT 58.914 40.909 30.87 0.00 39.42 2.71
3489 3673 3.508012 TGGCATGCCGTAAGTTTAATGTT 59.492 39.130 30.87 0.00 39.42 2.71
3490 3674 3.857093 GGCATGCCGTAAGTTTAATGTTG 59.143 43.478 23.48 0.00 0.00 3.33
3491 3675 4.380023 GGCATGCCGTAAGTTTAATGTTGA 60.380 41.667 23.48 0.00 0.00 3.18
3492 3676 5.339990 GCATGCCGTAAGTTTAATGTTGAT 58.660 37.500 6.36 0.00 0.00 2.57
3493 3677 5.455525 GCATGCCGTAAGTTTAATGTTGATC 59.544 40.000 6.36 0.00 0.00 2.92
3494 3678 5.554822 TGCCGTAAGTTTAATGTTGATCC 57.445 39.130 0.00 0.00 0.00 3.36
3495 3679 5.250200 TGCCGTAAGTTTAATGTTGATCCT 58.750 37.500 0.00 0.00 0.00 3.24
3496 3680 5.708230 TGCCGTAAGTTTAATGTTGATCCTT 59.292 36.000 0.00 0.00 0.00 3.36
3497 3681 6.027749 GCCGTAAGTTTAATGTTGATCCTTG 58.972 40.000 0.00 0.00 0.00 3.61
3498 3682 6.027749 CCGTAAGTTTAATGTTGATCCTTGC 58.972 40.000 0.00 0.00 0.00 4.01
3499 3683 6.348950 CCGTAAGTTTAATGTTGATCCTTGCA 60.349 38.462 0.00 0.00 0.00 4.08
3500 3684 7.250569 CGTAAGTTTAATGTTGATCCTTGCAT 58.749 34.615 0.00 0.00 0.00 3.96
3501 3685 7.429340 CGTAAGTTTAATGTTGATCCTTGCATC 59.571 37.037 0.00 0.00 0.00 3.91
3502 3686 7.472334 AAGTTTAATGTTGATCCTTGCATCT 57.528 32.000 0.00 0.00 0.00 2.90
3503 3687 6.860080 AGTTTAATGTTGATCCTTGCATCTG 58.140 36.000 0.00 0.00 0.00 2.90
3504 3688 6.435277 AGTTTAATGTTGATCCTTGCATCTGT 59.565 34.615 0.00 0.00 0.00 3.41
3505 3689 6.839124 TTAATGTTGATCCTTGCATCTGTT 57.161 33.333 0.00 0.00 0.00 3.16
3506 3690 4.713824 ATGTTGATCCTTGCATCTGTTG 57.286 40.909 0.00 0.00 0.00 3.33
3507 3691 3.753815 TGTTGATCCTTGCATCTGTTGA 58.246 40.909 0.00 0.00 0.00 3.18
3508 3692 4.338012 TGTTGATCCTTGCATCTGTTGAT 58.662 39.130 0.00 0.00 0.00 2.57
3509 3693 4.768448 TGTTGATCCTTGCATCTGTTGATT 59.232 37.500 0.00 0.00 0.00 2.57
3510 3694 5.244402 TGTTGATCCTTGCATCTGTTGATTT 59.756 36.000 0.00 0.00 0.00 2.17
3511 3695 6.433716 TGTTGATCCTTGCATCTGTTGATTTA 59.566 34.615 0.00 0.00 0.00 1.40
3512 3696 7.123098 TGTTGATCCTTGCATCTGTTGATTTAT 59.877 33.333 0.00 0.00 0.00 1.40
3513 3697 7.649533 TGATCCTTGCATCTGTTGATTTATT 57.350 32.000 0.00 0.00 0.00 1.40
3514 3698 7.485810 TGATCCTTGCATCTGTTGATTTATTG 58.514 34.615 0.00 0.00 0.00 1.90
3515 3699 5.653507 TCCTTGCATCTGTTGATTTATTGC 58.346 37.500 0.00 0.00 0.00 3.56
3516 3700 5.185442 TCCTTGCATCTGTTGATTTATTGCA 59.815 36.000 0.00 0.00 0.00 4.08
3517 3701 5.290158 CCTTGCATCTGTTGATTTATTGCAC 59.710 40.000 0.00 0.00 29.99 4.57
3518 3702 4.746729 TGCATCTGTTGATTTATTGCACC 58.253 39.130 0.00 0.00 0.00 5.01
3519 3703 4.463539 TGCATCTGTTGATTTATTGCACCT 59.536 37.500 0.00 0.00 0.00 4.00
3520 3704 5.047164 TGCATCTGTTGATTTATTGCACCTT 60.047 36.000 0.00 0.00 0.00 3.50
3521 3705 5.290158 GCATCTGTTGATTTATTGCACCTTG 59.710 40.000 0.00 0.00 0.00 3.61
3522 3706 6.623486 CATCTGTTGATTTATTGCACCTTGA 58.377 36.000 0.00 0.00 0.00 3.02
3523 3707 6.647334 TCTGTTGATTTATTGCACCTTGAA 57.353 33.333 0.00 0.00 0.00 2.69
3524 3708 6.680810 TCTGTTGATTTATTGCACCTTGAAG 58.319 36.000 0.00 0.00 0.00 3.02
3525 3709 6.265196 TCTGTTGATTTATTGCACCTTGAAGT 59.735 34.615 0.00 0.00 0.00 3.01
3526 3710 7.446931 TCTGTTGATTTATTGCACCTTGAAGTA 59.553 33.333 0.00 0.00 0.00 2.24
3527 3711 8.121305 TGTTGATTTATTGCACCTTGAAGTAT 57.879 30.769 0.00 0.00 0.00 2.12
3528 3712 8.028354 TGTTGATTTATTGCACCTTGAAGTATG 58.972 33.333 0.00 0.00 0.00 2.39
3529 3713 7.936496 TGATTTATTGCACCTTGAAGTATGA 57.064 32.000 0.00 0.00 0.00 2.15
3530 3714 8.347004 TGATTTATTGCACCTTGAAGTATGAA 57.653 30.769 0.00 0.00 0.00 2.57
3531 3715 8.243426 TGATTTATTGCACCTTGAAGTATGAAC 58.757 33.333 0.00 0.00 0.00 3.18
3532 3716 7.517614 TTTATTGCACCTTGAAGTATGAACA 57.482 32.000 0.00 0.00 0.00 3.18
3533 3717 7.701539 TTATTGCACCTTGAAGTATGAACAT 57.298 32.000 0.00 0.00 0.00 2.71
3534 3718 5.375417 TTGCACCTTGAAGTATGAACATG 57.625 39.130 0.00 0.00 0.00 3.21
3535 3719 4.397420 TGCACCTTGAAGTATGAACATGT 58.603 39.130 0.00 0.00 0.00 3.21
3536 3720 4.216042 TGCACCTTGAAGTATGAACATGTG 59.784 41.667 0.00 0.00 0.00 3.21
3537 3721 4.455533 GCACCTTGAAGTATGAACATGTGA 59.544 41.667 0.00 0.00 0.00 3.58
3538 3722 5.124457 GCACCTTGAAGTATGAACATGTGAT 59.876 40.000 0.00 0.00 0.00 3.06
3539 3723 6.316140 GCACCTTGAAGTATGAACATGTGATA 59.684 38.462 0.00 0.00 0.00 2.15
3540 3724 7.466455 GCACCTTGAAGTATGAACATGTGATAG 60.466 40.741 0.00 0.00 0.00 2.08
3541 3725 7.550551 CACCTTGAAGTATGAACATGTGATAGT 59.449 37.037 0.00 0.00 0.00 2.12
3542 3726 8.758829 ACCTTGAAGTATGAACATGTGATAGTA 58.241 33.333 0.00 0.00 0.00 1.82
3543 3727 9.599866 CCTTGAAGTATGAACATGTGATAGTAA 57.400 33.333 0.00 0.00 0.00 2.24
3558 3742 7.120923 GTGATAGTAAACTTATCACAGGGGA 57.879 40.000 16.41 0.00 45.52 4.81
3559 3743 7.210873 GTGATAGTAAACTTATCACAGGGGAG 58.789 42.308 16.41 0.00 45.52 4.30
3560 3744 7.069578 GTGATAGTAAACTTATCACAGGGGAGA 59.930 40.741 16.41 0.00 45.52 3.71
3561 3745 5.941555 AGTAAACTTATCACAGGGGAGAG 57.058 43.478 0.00 0.00 0.00 3.20
3562 3746 3.636153 AAACTTATCACAGGGGAGAGC 57.364 47.619 0.00 0.00 0.00 4.09
3563 3747 2.254152 ACTTATCACAGGGGAGAGCA 57.746 50.000 0.00 0.00 0.00 4.26
3564 3748 1.834263 ACTTATCACAGGGGAGAGCAC 59.166 52.381 0.00 0.00 0.00 4.40
3565 3749 1.139853 CTTATCACAGGGGAGAGCACC 59.860 57.143 0.00 0.00 38.12 5.01
3571 3755 2.363147 GGGGAGAGCACCTCGAGT 60.363 66.667 12.31 0.00 42.89 4.18
3581 3765 4.285851 CCTCGAGTGTTTGGAGGC 57.714 61.111 12.31 0.00 40.76 4.70
3582 3766 1.371183 CCTCGAGTGTTTGGAGGCA 59.629 57.895 12.31 0.00 40.76 4.75
3583 3767 0.951040 CCTCGAGTGTTTGGAGGCAC 60.951 60.000 12.31 0.00 40.76 5.01
3584 3768 0.951040 CTCGAGTGTTTGGAGGCACC 60.951 60.000 3.62 0.00 36.35 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.410631 TCACTATTGTTTCCTTCCGCA 57.589 42.857 0.00 0.00 0.00 5.69
49 50 6.254804 TGGTCACTATCGACAACATTATTTCG 59.745 38.462 0.00 0.00 37.66 3.46
63 64 1.226974 CCCGCTGTGGTCACTATCG 60.227 63.158 6.49 3.66 35.15 2.92
78 79 7.328277 TGAAATGGACTATGTTAAAATCCCG 57.672 36.000 0.00 0.00 0.00 5.14
215 222 9.277783 GGAGTACATTGCTTGATGTAATAATCT 57.722 33.333 8.89 3.79 42.39 2.40
290 297 6.715718 ACGCTGAAGGAATAAGCTATAGTCTA 59.284 38.462 0.84 0.00 34.72 2.59
291 298 5.536916 ACGCTGAAGGAATAAGCTATAGTCT 59.463 40.000 0.84 0.00 34.72 3.24
337 344 2.932187 GCCCCATGAATTGTTGCTTGAC 60.932 50.000 0.00 0.00 0.00 3.18
355 362 0.393537 CCACCTGATTGAGTGAGCCC 60.394 60.000 0.00 0.00 36.01 5.19
361 368 2.671070 CCGCCCACCTGATTGAGT 59.329 61.111 0.00 0.00 0.00 3.41
383 390 9.790344 CAGTAGGAAATCAGAATAGAATTGGAT 57.210 33.333 0.00 0.00 0.00 3.41
593 723 1.835494 ACTAGAGAAGTGCGGCACTA 58.165 50.000 33.53 17.94 44.62 2.74
633 765 3.646736 AAGGGATACAAGGGCAAGTAC 57.353 47.619 0.00 0.00 39.74 2.73
694 826 4.487948 CGCCAATCAACATTCAACAGAAT 58.512 39.130 0.00 0.00 32.33 2.40
767 899 5.163385 CCCCACTTGCATGAAACATCATTAT 60.163 40.000 6.60 0.00 0.00 1.28
770 902 2.498481 CCCCACTTGCATGAAACATCAT 59.502 45.455 6.60 0.00 0.00 2.45
887 1025 0.033090 AAACAAGACGGGGAGACGAC 59.967 55.000 0.00 0.00 37.61 4.34
972 1110 2.914908 GCGCCACCACAACGGAAAT 61.915 57.895 0.00 0.00 38.63 2.17
1042 1180 2.112297 AAAAAGCGCTCGGGGACA 59.888 55.556 12.06 0.00 0.00 4.02
1058 1196 4.533707 ACTGGGACTCAGATGAAGATGAAA 59.466 41.667 9.98 0.00 46.18 2.69
1090 1228 3.820467 AGAAGCAACATGAATCGAACCAA 59.180 39.130 0.00 0.00 0.00 3.67
1122 1260 2.683859 CCTCGGTCAGTACGCGACA 61.684 63.158 15.93 0.00 34.97 4.35
1130 1268 0.321653 GCACCAAATCCTCGGTCAGT 60.322 55.000 0.00 0.00 31.41 3.41
1150 1288 3.499338 TGTCCCTGCAAAGATGAAACAT 58.501 40.909 0.00 0.00 0.00 2.71
1197 1335 0.613260 CCTTCTTGATGTCGGGGTGA 59.387 55.000 0.00 0.00 0.00 4.02
1207 1345 1.645710 ACCACGGAGACCTTCTTGAT 58.354 50.000 0.00 0.00 0.00 2.57
1290 1428 1.714794 AGGAAACTCATCTCGCAACG 58.285 50.000 0.00 0.00 32.90 4.10
1313 1451 5.623956 AACCATATCAGGACACGGAATTA 57.376 39.130 0.00 0.00 0.00 1.40
1319 1457 4.060038 AGCTAAACCATATCAGGACACG 57.940 45.455 0.00 0.00 0.00 4.49
1339 1477 3.689161 TGCCGATCTGTAATTCAACCAAG 59.311 43.478 0.00 0.00 0.00 3.61
1400 1538 1.207329 GAGGGGAGACGTGCAACTTAT 59.793 52.381 0.00 0.00 31.75 1.73
1441 1579 2.713863 ACGAGTAAACCAACACCCAA 57.286 45.000 0.00 0.00 0.00 4.12
1442 1580 2.713863 AACGAGTAAACCAACACCCA 57.286 45.000 0.00 0.00 0.00 4.51
1443 1581 3.208594 AGAAACGAGTAAACCAACACCC 58.791 45.455 0.00 0.00 0.00 4.61
1444 1582 4.212004 GGTAGAAACGAGTAAACCAACACC 59.788 45.833 0.00 0.00 0.00 4.16
1445 1583 4.084900 CGGTAGAAACGAGTAAACCAACAC 60.085 45.833 0.00 0.00 0.00 3.32
1446 1584 4.050553 CGGTAGAAACGAGTAAACCAACA 58.949 43.478 0.00 0.00 0.00 3.33
1447 1585 3.120889 GCGGTAGAAACGAGTAAACCAAC 60.121 47.826 0.00 0.00 0.00 3.77
1448 1586 3.059166 GCGGTAGAAACGAGTAAACCAA 58.941 45.455 0.00 0.00 0.00 3.67
1449 1587 2.297033 AGCGGTAGAAACGAGTAAACCA 59.703 45.455 0.00 0.00 0.00 3.67
1450 1588 2.951726 AGCGGTAGAAACGAGTAAACC 58.048 47.619 0.00 0.00 0.00 3.27
1451 1589 4.209911 ACAAAGCGGTAGAAACGAGTAAAC 59.790 41.667 0.00 0.00 0.00 2.01
1452 1590 4.370917 ACAAAGCGGTAGAAACGAGTAAA 58.629 39.130 0.00 0.00 0.00 2.01
1453 1591 3.981211 ACAAAGCGGTAGAAACGAGTAA 58.019 40.909 0.00 0.00 0.00 2.24
1454 1592 3.568538 GACAAAGCGGTAGAAACGAGTA 58.431 45.455 0.00 0.00 0.00 2.59
1455 1593 2.401351 GACAAAGCGGTAGAAACGAGT 58.599 47.619 0.00 0.00 0.00 4.18
1456 1594 1.725164 GGACAAAGCGGTAGAAACGAG 59.275 52.381 0.00 0.00 0.00 4.18
1457 1595 1.606224 GGGACAAAGCGGTAGAAACGA 60.606 52.381 0.00 0.00 0.00 3.85
1458 1596 0.794473 GGGACAAAGCGGTAGAAACG 59.206 55.000 0.00 0.00 0.00 3.60
1459 1597 1.162698 GGGGACAAAGCGGTAGAAAC 58.837 55.000 0.00 0.00 0.00 2.78
1460 1598 0.037160 GGGGGACAAAGCGGTAGAAA 59.963 55.000 0.00 0.00 0.00 2.52
1461 1599 1.128809 TGGGGGACAAAGCGGTAGAA 61.129 55.000 0.00 0.00 0.00 2.10
1462 1600 0.912487 ATGGGGGACAAAGCGGTAGA 60.912 55.000 0.00 0.00 0.00 2.59
1463 1601 0.463833 GATGGGGGACAAAGCGGTAG 60.464 60.000 0.00 0.00 0.00 3.18
1464 1602 1.605453 GATGGGGGACAAAGCGGTA 59.395 57.895 0.00 0.00 0.00 4.02
1465 1603 2.355115 GATGGGGGACAAAGCGGT 59.645 61.111 0.00 0.00 0.00 5.68
1466 1604 2.440247 GGATGGGGGACAAAGCGG 60.440 66.667 0.00 0.00 0.00 5.52
1467 1605 2.824041 CGGATGGGGGACAAAGCG 60.824 66.667 0.00 0.00 0.00 4.68
1468 1606 3.140814 GCGGATGGGGGACAAAGC 61.141 66.667 0.00 0.00 0.00 3.51
1469 1607 2.440247 GGCGGATGGGGGACAAAG 60.440 66.667 0.00 0.00 0.00 2.77
1470 1608 2.938798 AGGCGGATGGGGGACAAA 60.939 61.111 0.00 0.00 0.00 2.83
1471 1609 3.407967 GAGGCGGATGGGGGACAA 61.408 66.667 0.00 0.00 0.00 3.18
1472 1610 4.414956 AGAGGCGGATGGGGGACA 62.415 66.667 0.00 0.00 0.00 4.02
1506 1646 4.927782 TCGCAGCGCCACCAGTTT 62.928 61.111 10.87 0.00 0.00 2.66
1516 1656 0.459237 AGGAAACTCATCTCGCAGCG 60.459 55.000 9.06 9.06 32.90 5.18
1536 1676 4.447724 CCATATCAGGACACGGAATTAACG 59.552 45.833 0.92 0.92 37.36 3.18
1539 1679 5.623956 AACCATATCAGGACACGGAATTA 57.376 39.130 0.00 0.00 0.00 1.40
1565 1705 3.689161 TGCCGATCTGTAATTCAACCAAG 59.311 43.478 0.00 0.00 0.00 3.61
1626 1766 2.173569 GGAGGGGAGACATGCAACTTAT 59.826 50.000 0.00 0.00 0.00 1.73
1669 1809 3.725490 AGAAACGAGTAAACTGACACCC 58.275 45.455 0.00 0.00 0.00 4.61
1684 1824 6.812160 ACACTAGGCAAACTAAGATAGAAACG 59.188 38.462 0.00 0.00 0.00 3.60
1691 1831 5.401531 TCGAACACTAGGCAAACTAAGAT 57.598 39.130 0.00 0.00 0.00 2.40
1861 2001 1.877637 TCACTGCAACACATTACGCT 58.122 45.000 0.00 0.00 0.00 5.07
1962 2106 2.668945 GCTTTTCGTTCTCCAGCTAGTC 59.331 50.000 0.00 0.00 0.00 2.59
2078 2223 5.964758 TGCATCCATTTCCAAATAGAACAC 58.035 37.500 0.00 0.00 0.00 3.32
2113 2258 1.300931 GCCAGACGTGTGCAAGAGA 60.301 57.895 7.28 0.00 0.00 3.10
2183 2328 4.807039 GTGGTCGCCGCCGTACAT 62.807 66.667 0.00 0.00 35.54 2.29
2258 2404 4.253685 TCTAAACCAACAGAGCATGCTAC 58.746 43.478 22.74 14.27 0.00 3.58
2298 2444 5.051240 GCTGTTTAGTACGCATACATGGTAC 60.051 44.000 0.00 0.00 36.03 3.34
2367 2518 4.501400 GGCTACCACAAGCAAAAGTGAAAT 60.501 41.667 0.00 0.00 44.64 2.17
2369 2520 2.360801 GGCTACCACAAGCAAAAGTGAA 59.639 45.455 0.00 0.00 44.64 3.18
2514 2669 5.311265 ACCATAATATGACAGCAGACCATG 58.689 41.667 1.10 0.00 0.00 3.66
2604 2760 1.303643 GGTAGCAGCCAAGCCAGTT 60.304 57.895 0.00 0.00 34.23 3.16
2673 2830 6.849085 ACAGAGGGAATATCTGCTACTATG 57.151 41.667 2.96 0.00 46.64 2.23
2766 2933 8.263940 TCATGCATCATATCACATCACATAAG 57.736 34.615 0.00 0.00 0.00 1.73
2787 2954 6.127810 ACTCCATGTCGAATTGAAATCATG 57.872 37.500 0.00 0.00 31.63 3.07
2795 2962 4.455533 TCAGGAAAACTCCATGTCGAATTG 59.544 41.667 0.00 0.00 0.00 2.32
2850 3018 7.988028 GGCACAAGACCTCTTTAATCTAGTTAT 59.012 37.037 0.00 0.00 33.11 1.89
2856 3024 3.330701 TGGGCACAAGACCTCTTTAATCT 59.669 43.478 0.00 0.00 46.30 2.40
2916 3084 8.193953 AGCCCAATTATTTGTCCAATATTAGG 57.806 34.615 0.00 0.00 0.00 2.69
3070 3247 1.272203 ACCATACCCAACAATTCGGCA 60.272 47.619 0.00 0.00 0.00 5.69
3090 3267 4.764050 TCCCTATTAATTTCAGCGTGGA 57.236 40.909 0.00 0.00 0.00 4.02
3113 3291 6.258507 GCCCAACAATTCAGCCTTTTATATTG 59.741 38.462 0.00 0.00 0.00 1.90
3141 3324 2.279935 TTCGGTGTTTTACATGGGCT 57.720 45.000 0.00 0.00 0.00 5.19
3231 3414 0.682852 CCCACACCAAGTCGGAACTA 59.317 55.000 0.00 0.00 38.63 2.24
3234 3417 2.112297 GCCCACACCAAGTCGGAA 59.888 61.111 0.00 0.00 38.63 4.30
3241 3424 0.840617 TAGTTGTCTGCCCACACCAA 59.159 50.000 0.00 0.00 0.00 3.67
3245 3428 1.070134 GTCACTAGTTGTCTGCCCACA 59.930 52.381 0.00 0.00 0.00 4.17
3246 3429 1.608283 GGTCACTAGTTGTCTGCCCAC 60.608 57.143 0.00 0.00 0.00 4.61
3284 3467 5.823353 GACCAAAACAAAAGGTCGTTGATA 58.177 37.500 0.00 0.00 42.02 2.15
3334 3517 8.680001 AGTCGTAAACTGAAATTAACAACCTTT 58.320 29.630 0.00 0.00 36.65 3.11
3465 3649 1.080298 TAAACTTACGGCATGCCACG 58.920 50.000 34.93 24.12 35.37 4.94
3469 3653 4.728534 TCAACATTAAACTTACGGCATGC 58.271 39.130 9.90 9.90 0.00 4.06
3472 3656 5.250200 AGGATCAACATTAAACTTACGGCA 58.750 37.500 0.00 0.00 0.00 5.69
3473 3657 5.813080 AGGATCAACATTAAACTTACGGC 57.187 39.130 0.00 0.00 0.00 5.68
3474 3658 6.027749 GCAAGGATCAACATTAAACTTACGG 58.972 40.000 0.00 0.00 0.00 4.02
3475 3659 6.607689 TGCAAGGATCAACATTAAACTTACG 58.392 36.000 0.00 0.00 0.00 3.18
3476 3660 8.462016 AGATGCAAGGATCAACATTAAACTTAC 58.538 33.333 4.40 0.00 0.00 2.34
3477 3661 8.461222 CAGATGCAAGGATCAACATTAAACTTA 58.539 33.333 4.40 0.00 0.00 2.24
3478 3662 7.039504 ACAGATGCAAGGATCAACATTAAACTT 60.040 33.333 4.40 0.00 0.00 2.66
3479 3663 6.435277 ACAGATGCAAGGATCAACATTAAACT 59.565 34.615 4.40 0.00 0.00 2.66
3480 3664 6.624423 ACAGATGCAAGGATCAACATTAAAC 58.376 36.000 4.40 0.00 0.00 2.01
3481 3665 6.839124 ACAGATGCAAGGATCAACATTAAA 57.161 33.333 4.40 0.00 0.00 1.52
3482 3666 6.433716 TCAACAGATGCAAGGATCAACATTAA 59.566 34.615 4.40 0.00 0.00 1.40
3483 3667 5.945191 TCAACAGATGCAAGGATCAACATTA 59.055 36.000 4.40 0.00 0.00 1.90
3484 3668 4.768448 TCAACAGATGCAAGGATCAACATT 59.232 37.500 4.40 0.00 0.00 2.71
3485 3669 4.338012 TCAACAGATGCAAGGATCAACAT 58.662 39.130 4.40 0.00 0.00 2.71
3486 3670 3.753815 TCAACAGATGCAAGGATCAACA 58.246 40.909 4.40 0.00 0.00 3.33
3487 3671 4.978083 ATCAACAGATGCAAGGATCAAC 57.022 40.909 4.40 0.00 0.00 3.18
3488 3672 5.988310 AAATCAACAGATGCAAGGATCAA 57.012 34.783 4.40 0.00 0.00 2.57
3489 3673 7.485810 CAATAAATCAACAGATGCAAGGATCA 58.514 34.615 4.40 0.00 0.00 2.92
3490 3674 6.420008 GCAATAAATCAACAGATGCAAGGATC 59.580 38.462 0.00 0.00 32.80 3.36
3491 3675 6.127281 TGCAATAAATCAACAGATGCAAGGAT 60.127 34.615 0.00 0.00 39.15 3.24
3492 3676 5.185442 TGCAATAAATCAACAGATGCAAGGA 59.815 36.000 0.00 0.00 39.15 3.36
3493 3677 5.290158 GTGCAATAAATCAACAGATGCAAGG 59.710 40.000 0.00 0.00 43.10 3.61
3494 3678 5.290158 GGTGCAATAAATCAACAGATGCAAG 59.710 40.000 0.00 0.00 43.10 4.01
3495 3679 5.047164 AGGTGCAATAAATCAACAGATGCAA 60.047 36.000 0.00 0.00 43.10 4.08
3496 3680 4.463539 AGGTGCAATAAATCAACAGATGCA 59.536 37.500 0.00 0.00 39.73 3.96
3497 3681 5.002464 AGGTGCAATAAATCAACAGATGC 57.998 39.130 0.00 0.00 0.00 3.91
3498 3682 6.623486 TCAAGGTGCAATAAATCAACAGATG 58.377 36.000 0.00 0.00 0.00 2.90
3499 3683 6.839124 TCAAGGTGCAATAAATCAACAGAT 57.161 33.333 0.00 0.00 0.00 2.90
3500 3684 6.265196 ACTTCAAGGTGCAATAAATCAACAGA 59.735 34.615 0.00 0.00 0.00 3.41
3501 3685 6.449698 ACTTCAAGGTGCAATAAATCAACAG 58.550 36.000 0.00 0.00 0.00 3.16
3502 3686 6.403866 ACTTCAAGGTGCAATAAATCAACA 57.596 33.333 0.00 0.00 0.00 3.33
3503 3687 8.243426 TCATACTTCAAGGTGCAATAAATCAAC 58.757 33.333 0.00 0.00 0.00 3.18
3504 3688 8.347004 TCATACTTCAAGGTGCAATAAATCAA 57.653 30.769 0.00 0.00 0.00 2.57
3505 3689 7.936496 TCATACTTCAAGGTGCAATAAATCA 57.064 32.000 0.00 0.00 0.00 2.57
3506 3690 8.243426 TGTTCATACTTCAAGGTGCAATAAATC 58.757 33.333 0.00 0.00 0.00 2.17
3507 3691 8.121305 TGTTCATACTTCAAGGTGCAATAAAT 57.879 30.769 0.00 0.00 0.00 1.40
3508 3692 7.517614 TGTTCATACTTCAAGGTGCAATAAA 57.482 32.000 0.00 0.00 0.00 1.40
3509 3693 7.176515 ACATGTTCATACTTCAAGGTGCAATAA 59.823 33.333 0.00 0.00 0.00 1.40
3510 3694 6.658816 ACATGTTCATACTTCAAGGTGCAATA 59.341 34.615 0.00 0.00 0.00 1.90
3511 3695 5.477984 ACATGTTCATACTTCAAGGTGCAAT 59.522 36.000 0.00 0.00 0.00 3.56
3512 3696 4.826733 ACATGTTCATACTTCAAGGTGCAA 59.173 37.500 0.00 0.00 0.00 4.08
3513 3697 4.216042 CACATGTTCATACTTCAAGGTGCA 59.784 41.667 0.00 0.00 0.00 4.57
3514 3698 4.455533 TCACATGTTCATACTTCAAGGTGC 59.544 41.667 0.00 0.00 0.00 5.01
3515 3699 6.748333 ATCACATGTTCATACTTCAAGGTG 57.252 37.500 0.00 0.00 0.00 4.00
3516 3700 7.624549 ACTATCACATGTTCATACTTCAAGGT 58.375 34.615 0.00 0.00 0.00 3.50
3517 3701 9.599866 TTACTATCACATGTTCATACTTCAAGG 57.400 33.333 0.00 0.00 0.00 3.61
3534 3718 7.069578 TCTCCCCTGTGATAAGTTTACTATCAC 59.930 40.741 13.55 13.55 46.07 3.06
3535 3719 7.130099 TCTCCCCTGTGATAAGTTTACTATCA 58.870 38.462 0.00 0.00 0.00 2.15
3536 3720 7.598759 TCTCCCCTGTGATAAGTTTACTATC 57.401 40.000 0.00 0.00 0.00 2.08
3537 3721 6.042208 GCTCTCCCCTGTGATAAGTTTACTAT 59.958 42.308 0.00 0.00 0.00 2.12
3538 3722 5.363005 GCTCTCCCCTGTGATAAGTTTACTA 59.637 44.000 0.00 0.00 0.00 1.82
3539 3723 4.162509 GCTCTCCCCTGTGATAAGTTTACT 59.837 45.833 0.00 0.00 0.00 2.24
3540 3724 4.081087 TGCTCTCCCCTGTGATAAGTTTAC 60.081 45.833 0.00 0.00 0.00 2.01
3541 3725 4.081087 GTGCTCTCCCCTGTGATAAGTTTA 60.081 45.833 0.00 0.00 0.00 2.01
3542 3726 2.912956 TGCTCTCCCCTGTGATAAGTTT 59.087 45.455 0.00 0.00 0.00 2.66
3543 3727 2.237392 GTGCTCTCCCCTGTGATAAGTT 59.763 50.000 0.00 0.00 0.00 2.66
3544 3728 1.834263 GTGCTCTCCCCTGTGATAAGT 59.166 52.381 0.00 0.00 0.00 2.24
3545 3729 1.139853 GGTGCTCTCCCCTGTGATAAG 59.860 57.143 0.00 0.00 0.00 1.73
3546 3730 1.204146 GGTGCTCTCCCCTGTGATAA 58.796 55.000 0.00 0.00 0.00 1.75
3547 3731 0.339859 AGGTGCTCTCCCCTGTGATA 59.660 55.000 0.00 0.00 0.00 2.15
3548 3732 0.980231 GAGGTGCTCTCCCCTGTGAT 60.980 60.000 0.00 0.00 36.52 3.06
3549 3733 1.610673 GAGGTGCTCTCCCCTGTGA 60.611 63.158 0.00 0.00 36.52 3.58
3550 3734 2.985456 GAGGTGCTCTCCCCTGTG 59.015 66.667 0.00 0.00 36.52 3.66
3551 3735 2.681778 CGAGGTGCTCTCCCCTGT 60.682 66.667 0.00 0.00 39.30 4.00
3552 3736 2.363018 TCGAGGTGCTCTCCCCTG 60.363 66.667 0.00 0.00 39.30 4.45
3553 3737 2.043450 CTCGAGGTGCTCTCCCCT 60.043 66.667 3.91 0.00 39.30 4.79
3554 3738 2.363147 ACTCGAGGTGCTCTCCCC 60.363 66.667 18.41 0.00 39.30 4.81
3555 3739 2.888863 CACTCGAGGTGCTCTCCC 59.111 66.667 18.41 0.00 39.30 4.30
3563 3747 1.371558 GCCTCCAAACACTCGAGGT 59.628 57.895 18.41 9.05 44.32 3.85
3564 3748 0.951040 GTGCCTCCAAACACTCGAGG 60.951 60.000 18.41 8.36 45.12 4.63
3565 3749 0.951040 GGTGCCTCCAAACACTCGAG 60.951 60.000 11.84 11.84 36.99 4.04
3566 3750 1.070786 GGTGCCTCCAAACACTCGA 59.929 57.895 0.00 0.00 36.99 4.04
3567 3751 1.227823 TGGTGCCTCCAAACACTCG 60.228 57.895 0.00 0.00 44.12 4.18
3568 3752 4.898607 TGGTGCCTCCAAACACTC 57.101 55.556 0.00 0.00 44.12 3.51


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

AutoCloner maintained by Alex Coulton.