Multiple sequence alignment - TraesCS2D01G105300

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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 TraesCS2D01G105300 chr2D 100.000 8722 0 0 1 8722 56638691 56647412 0.000000e+00 16107.0
1 TraesCS2D01G105300 chr2D 87.405 262 30 3 4712 4972 485982856 485982597 1.840000e-76 298.0
2 TraesCS2D01G105300 chr2D 94.382 89 5 0 8634 8722 56667752 56667840 4.250000e-28 137.0
3 TraesCS2D01G105300 chr2D 92.135 89 7 0 8634 8722 56654173 56654261 9.190000e-25 126.0
4 TraesCS2D01G105300 chr2A 94.506 3531 129 43 4851 8363 58016151 58019634 0.000000e+00 5385.0
5 TraesCS2D01G105300 chr2A 90.635 3385 152 72 706 3998 58012097 58015408 0.000000e+00 4342.0
6 TraesCS2D01G105300 chr2A 83.216 566 33 22 1007 1532 595998196 595998739 6.170000e-126 462.0
7 TraesCS2D01G105300 chr2A 88.421 285 15 6 3999 4265 58015500 58015784 2.350000e-85 327.0
8 TraesCS2D01G105300 chr2A 85.185 189 10 4 410 593 58011848 58012023 2.500000e-40 178.0
9 TraesCS2D01G105300 chr2A 83.251 203 15 9 43 245 58011575 58011758 1.510000e-37 169.0
10 TraesCS2D01G105300 chr2A 98.876 89 1 0 8634 8722 58020087 58020175 9.060000e-35 159.0
11 TraesCS2D01G105300 chr2A 95.455 88 4 0 8635 8722 58092056 58092143 3.280000e-29 141.0
12 TraesCS2D01G105300 chr2A 100.000 30 0 0 1 30 58011557 58011586 1.000000e-03 56.5
13 TraesCS2D01G105300 chr2B 88.650 4088 192 100 35 3998 89701440 89705379 0.000000e+00 4728.0
14 TraesCS2D01G105300 chr2B 94.695 1885 79 13 6275 8157 89707864 89709729 0.000000e+00 2907.0
15 TraesCS2D01G105300 chr2B 94.404 1787 75 13 4316 6098 89705970 89707735 0.000000e+00 2723.0
16 TraesCS2D01G105300 chr2B 83.117 616 56 18 1130 1740 137442981 137442409 1.300000e-142 518.0
17 TraesCS2D01G105300 chr2B 79.094 684 82 28 889 1543 66809504 66808853 1.750000e-111 414.0
18 TraesCS2D01G105300 chr2B 83.081 396 37 12 8352 8719 89709778 89710171 5.050000e-87 333.0
19 TraesCS2D01G105300 chr2B 87.368 285 18 6 3999 4265 89705472 89705756 2.360000e-80 311.0
20 TraesCS2D01G105300 chr2B 92.135 89 7 0 8634 8722 89959888 89959976 9.190000e-25 126.0
21 TraesCS2D01G105300 chr2B 95.455 66 3 0 6213 6278 89707728 89707793 1.200000e-18 106.0
22 TraesCS2D01G105300 chr7A 85.918 561 33 17 1004 1532 613710601 613711147 2.750000e-154 556.0
23 TraesCS2D01G105300 chr4D 86.742 528 34 19 1007 1532 198581610 198582103 9.890000e-154 555.0
24 TraesCS2D01G105300 chr4D 87.640 267 27 5 4708 4972 9306378 9306116 1.100000e-78 305.0
25 TraesCS2D01G105300 chr4D 87.452 263 31 2 4712 4973 145579507 145579768 1.420000e-77 302.0
26 TraesCS2D01G105300 chr6B 84.444 540 50 16 1013 1532 254030600 254030075 1.310000e-137 501.0
27 TraesCS2D01G105300 chr4A 83.574 554 47 21 1007 1532 658607454 658607991 6.120000e-131 479.0
28 TraesCS2D01G105300 chr4A 78.261 161 28 6 7988 8146 677971552 677971397 7.210000e-16 97.1
29 TraesCS2D01G105300 chr5B 83.303 557 41 21 1007 1532 386152530 386153065 4.770000e-127 466.0
30 TraesCS2D01G105300 chr3B 82.469 559 55 19 1007 1532 534149728 534149180 4.800000e-122 449.0
31 TraesCS2D01G105300 chr5D 83.093 485 50 18 1261 1741 15521774 15522230 6.300000e-111 412.0
32 TraesCS2D01G105300 chr6D 89.591 269 26 2 4709 4976 348087597 348087864 3.020000e-89 340.0
33 TraesCS2D01G105300 chr7D 88.235 272 28 3 4711 4981 363048924 363048656 1.090000e-83 322.0
34 TraesCS2D01G105300 chr7D 93.878 49 3 0 772 820 195262293 195262341 3.380000e-09 75.0
35 TraesCS2D01G105300 chr7B 88.806 268 20 7 4708 4972 504480178 504479918 3.930000e-83 320.0
36 TraesCS2D01G105300 chr7B 86.813 273 25 6 4711 4981 322488712 322488449 2.380000e-75 294.0
37 TraesCS2D01G105300 chr7B 88.333 60 5 2 8532 8591 387149310 387149253 4.370000e-08 71.3
38 TraesCS2D01G105300 chr4B 87.547 265 29 4 4710 4972 611856147 611855885 3.960000e-78 303.0
39 TraesCS2D01G105300 chr3A 80.606 165 27 4 7983 8146 624836099 624835939 1.190000e-23 122.0
40 TraesCS2D01G105300 chr1D 87.500 56 5 1 8532 8587 99702096 99702149 7.310000e-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 TraesCS2D01G105300 chr2D 56638691 56647412 8721 False 16107.000000 16107 100.000000 1 8722 1 chr2D.!!$F1 8721
1 TraesCS2D01G105300 chr2A 58011557 58020175 8618 False 1516.642857 5385 91.553429 1 8722 7 chr2A.!!$F3 8721
2 TraesCS2D01G105300 chr2A 595998196 595998739 543 False 462.000000 462 83.216000 1007 1532 1 chr2A.!!$F2 525
3 TraesCS2D01G105300 chr2B 89701440 89710171 8731 False 1851.333333 4728 90.608833 35 8719 6 chr2B.!!$F2 8684
4 TraesCS2D01G105300 chr2B 137442409 137442981 572 True 518.000000 518 83.117000 1130 1740 1 chr2B.!!$R2 610
5 TraesCS2D01G105300 chr2B 66808853 66809504 651 True 414.000000 414 79.094000 889 1543 1 chr2B.!!$R1 654
6 TraesCS2D01G105300 chr7A 613710601 613711147 546 False 556.000000 556 85.918000 1004 1532 1 chr7A.!!$F1 528
7 TraesCS2D01G105300 chr6B 254030075 254030600 525 True 501.000000 501 84.444000 1013 1532 1 chr6B.!!$R1 519
8 TraesCS2D01G105300 chr4A 658607454 658607991 537 False 479.000000 479 83.574000 1007 1532 1 chr4A.!!$F1 525
9 TraesCS2D01G105300 chr5B 386152530 386153065 535 False 466.000000 466 83.303000 1007 1532 1 chr5B.!!$F1 525
10 TraesCS2D01G105300 chr3B 534149180 534149728 548 True 449.000000 449 82.469000 1007 1532 1 chr3B.!!$R1 525

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
261 276 0.249489 CTCATTTCTACTCCGCCCCG 60.249 60.000 0.00 0.0 0.00 5.73 F
320 335 0.254178 CCTGGCTGTGATACAAGCCT 59.746 55.000 14.32 0.0 40.58 4.58 F
719 774 0.547712 CCTTGTCCTTCCCTCCCTCA 60.548 60.000 0.00 0.0 0.00 3.86 F
728 783 1.001641 CCCTCCCTCACTTGGCTTG 60.002 63.158 0.00 0.0 0.00 4.01 F
2360 2568 0.170561 CAGGTAGACCGTTGGAGTCG 59.829 60.000 0.00 0.0 42.08 4.18 F
3418 3626 1.051812 ATGAGCTCCCGGATGTTAGG 58.948 55.000 12.15 0.0 0.00 2.69 F
4422 4915 1.995376 ATTGGGAAAGCAACCGAAGT 58.005 45.000 0.00 0.0 0.00 3.01 F
4721 5215 2.163818 TGTTCTTTGTACTGCCTCCG 57.836 50.000 0.00 0.0 0.00 4.63 F
6000 6499 0.040514 TTGCTCAAAATGGCGTCGTG 60.041 50.000 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 1804 1.000938 GTTTCCTCAAGCAAGCACCAG 60.001 52.381 0.00 0.00 0.00 4.00 R
1919 2125 1.289066 CTCGAACGCCAACCTGAGA 59.711 57.895 0.00 0.00 0.00 3.27 R
2360 2568 0.249911 AATCGAGCATAAGGGACGGC 60.250 55.000 0.00 0.00 0.00 5.68 R
3037 3245 8.972262 TTGCACGTAAATAATTAAAGCATCAA 57.028 26.923 0.00 0.00 29.89 2.57 R
3770 3990 0.107312 CTGGCTGAGAGATTGGTGGG 60.107 60.000 0.00 0.00 0.00 4.61 R
5512 6009 0.321996 GGGCCTCCTCGTTATCCATC 59.678 60.000 0.84 0.00 0.00 3.51 R
5560 6057 0.532862 CAGGACGCAACAACTCCTGT 60.533 55.000 7.61 0.00 44.28 4.00 R
6673 7252 1.211969 GCAGGAACAGCTGCACATG 59.788 57.895 15.27 16.39 45.11 3.21 R
8107 8695 0.533755 CAAAAATGCGTTTGGCCCCA 60.534 50.000 4.29 0.00 42.61 4.96 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
64 65 3.681835 GTCGGCGTCTGGACTGGT 61.682 66.667 6.85 0.00 0.00 4.00
68 69 2.358737 GCGTCTGGACTGGTTGGG 60.359 66.667 0.00 0.00 0.00 4.12
256 271 2.035321 GCCTCCTCTCATTTCTACTCCG 59.965 54.545 0.00 0.00 0.00 4.63
257 272 2.035321 CCTCCTCTCATTTCTACTCCGC 59.965 54.545 0.00 0.00 0.00 5.54
260 275 1.069358 CTCTCATTTCTACTCCGCCCC 59.931 57.143 0.00 0.00 0.00 5.80
261 276 0.249489 CTCATTTCTACTCCGCCCCG 60.249 60.000 0.00 0.00 0.00 5.73
287 302 3.749088 ACGTCGGCAATAGAAAATGAACA 59.251 39.130 0.00 0.00 0.00 3.18
314 329 1.153086 CCTGGCCTGGCTGTGATAC 60.153 63.158 19.68 0.00 0.00 2.24
315 330 1.603842 CTGGCCTGGCTGTGATACA 59.396 57.895 19.68 4.98 0.00 2.29
318 333 1.379642 GGCCTGGCTGTGATACAAGC 61.380 60.000 19.68 0.00 0.00 4.01
319 334 1.379642 GCCTGGCTGTGATACAAGCC 61.380 60.000 12.43 6.75 40.45 4.35
320 335 0.254178 CCTGGCTGTGATACAAGCCT 59.746 55.000 14.32 0.00 40.58 4.58
440 489 1.202143 GCGGAAACCATAGGAAAAGCG 60.202 52.381 0.00 0.00 0.00 4.68
441 490 2.081462 CGGAAACCATAGGAAAAGCGT 58.919 47.619 0.00 0.00 0.00 5.07
443 492 2.415491 GGAAACCATAGGAAAAGCGTGC 60.415 50.000 0.00 0.00 0.00 5.34
498 551 1.999071 AACAAAAAGCCACGCTCGCA 61.999 50.000 0.00 0.00 38.25 5.10
499 552 1.727022 CAAAAAGCCACGCTCGCAG 60.727 57.895 0.00 0.00 38.25 5.18
500 553 2.186826 AAAAAGCCACGCTCGCAGT 61.187 52.632 0.00 0.00 38.25 4.40
501 554 1.724582 AAAAAGCCACGCTCGCAGTT 61.725 50.000 0.00 0.00 38.25 3.16
502 555 2.392613 AAAAGCCACGCTCGCAGTTG 62.393 55.000 0.00 0.00 38.25 3.16
506 559 3.349006 CACGCTCGCAGTTGGCTT 61.349 61.111 0.00 0.00 41.67 4.35
507 560 2.591715 ACGCTCGCAGTTGGCTTT 60.592 55.556 0.00 0.00 41.67 3.51
508 561 1.301401 ACGCTCGCAGTTGGCTTTA 60.301 52.632 0.00 0.00 41.67 1.85
509 562 1.132640 CGCTCGCAGTTGGCTTTAC 59.867 57.895 0.00 0.00 41.67 2.01
510 563 1.502190 GCTCGCAGTTGGCTTTACC 59.498 57.895 0.00 0.00 41.67 2.85
511 564 1.787847 CTCGCAGTTGGCTTTACCG 59.212 57.895 0.00 0.00 43.94 4.02
512 565 0.949105 CTCGCAGTTGGCTTTACCGT 60.949 55.000 0.00 0.00 43.94 4.83
523 576 1.463804 TTTACCGTCCCCAACCCCT 60.464 57.895 0.00 0.00 0.00 4.79
524 577 1.491274 TTTACCGTCCCCAACCCCTC 61.491 60.000 0.00 0.00 0.00 4.30
573 627 2.487762 CAGCTGGCTTTATTTCACGGAA 59.512 45.455 5.57 0.00 0.00 4.30
608 663 3.532542 CTCCTCAATCCCCTTTTCGTAC 58.467 50.000 0.00 0.00 0.00 3.67
611 666 4.161001 TCCTCAATCCCCTTTTCGTACTAC 59.839 45.833 0.00 0.00 0.00 2.73
613 668 5.361857 CCTCAATCCCCTTTTCGTACTACTA 59.638 44.000 0.00 0.00 0.00 1.82
614 669 6.461110 TCAATCCCCTTTTCGTACTACTAG 57.539 41.667 0.00 0.00 0.00 2.57
615 670 5.954150 TCAATCCCCTTTTCGTACTACTAGT 59.046 40.000 0.00 0.00 0.00 2.57
616 671 6.438425 TCAATCCCCTTTTCGTACTACTAGTT 59.562 38.462 0.00 0.00 0.00 2.24
618 673 6.029346 TCCCCTTTTCGTACTACTAGTTTG 57.971 41.667 0.00 0.00 0.00 2.93
620 675 5.047092 CCCCTTTTCGTACTACTAGTTTGGA 60.047 44.000 0.00 0.00 0.00 3.53
621 676 6.351626 CCCCTTTTCGTACTACTAGTTTGGAT 60.352 42.308 0.00 0.00 0.00 3.41
622 677 7.101700 CCCTTTTCGTACTACTAGTTTGGATT 58.898 38.462 0.00 0.00 0.00 3.01
624 679 8.440833 CCTTTTCGTACTACTAGTTTGGATTTG 58.559 37.037 0.00 0.00 0.00 2.32
626 681 6.839124 TCGTACTACTAGTTTGGATTTGGA 57.161 37.500 0.00 0.00 0.00 3.53
627 682 6.860080 TCGTACTACTAGTTTGGATTTGGAG 58.140 40.000 0.00 0.00 0.00 3.86
628 683 6.435277 TCGTACTACTAGTTTGGATTTGGAGT 59.565 38.462 0.00 0.00 0.00 3.85
629 684 7.611467 TCGTACTACTAGTTTGGATTTGGAGTA 59.389 37.037 0.00 0.00 0.00 2.59
630 685 7.914346 CGTACTACTAGTTTGGATTTGGAGTAG 59.086 40.741 0.00 0.00 40.35 2.57
631 686 7.793948 ACTACTAGTTTGGATTTGGAGTAGT 57.206 36.000 0.00 6.08 41.89 2.73
632 687 7.612677 ACTACTAGTTTGGATTTGGAGTAGTG 58.387 38.462 0.00 0.00 43.87 2.74
633 688 5.246307 ACTAGTTTGGATTTGGAGTAGTGC 58.754 41.667 0.00 0.00 29.56 4.40
634 689 4.373156 AGTTTGGATTTGGAGTAGTGCT 57.627 40.909 0.00 0.00 0.00 4.40
635 690 5.499004 AGTTTGGATTTGGAGTAGTGCTA 57.501 39.130 0.00 0.00 0.00 3.49
636 691 5.491982 AGTTTGGATTTGGAGTAGTGCTAG 58.508 41.667 0.00 0.00 0.00 3.42
637 692 5.013183 AGTTTGGATTTGGAGTAGTGCTAGT 59.987 40.000 0.00 0.00 0.00 2.57
638 693 6.212791 AGTTTGGATTTGGAGTAGTGCTAGTA 59.787 38.462 0.00 0.00 0.00 1.82
639 694 5.854010 TGGATTTGGAGTAGTGCTAGTAG 57.146 43.478 0.00 0.00 0.00 2.57
640 695 5.269991 TGGATTTGGAGTAGTGCTAGTAGT 58.730 41.667 0.00 0.00 0.00 2.73
641 696 5.127194 TGGATTTGGAGTAGTGCTAGTAGTG 59.873 44.000 0.00 0.00 0.00 2.74
642 697 5.127356 GGATTTGGAGTAGTGCTAGTAGTGT 59.873 44.000 0.00 0.00 0.00 3.55
643 698 5.386958 TTTGGAGTAGTGCTAGTAGTGTG 57.613 43.478 0.00 0.00 0.00 3.82
644 699 3.353557 TGGAGTAGTGCTAGTAGTGTGG 58.646 50.000 0.00 0.00 0.00 4.17
645 700 2.688958 GGAGTAGTGCTAGTAGTGTGGG 59.311 54.545 0.00 0.00 0.00 4.61
646 701 3.618351 GAGTAGTGCTAGTAGTGTGGGA 58.382 50.000 0.00 0.00 0.00 4.37
647 702 3.622630 AGTAGTGCTAGTAGTGTGGGAG 58.377 50.000 0.00 0.00 0.00 4.30
648 703 2.606751 AGTGCTAGTAGTGTGGGAGT 57.393 50.000 0.00 0.00 0.00 3.85
649 704 2.171840 AGTGCTAGTAGTGTGGGAGTG 58.828 52.381 0.00 0.00 0.00 3.51
650 705 0.895530 TGCTAGTAGTGTGGGAGTGC 59.104 55.000 0.00 0.00 0.00 4.40
651 706 1.187087 GCTAGTAGTGTGGGAGTGCT 58.813 55.000 0.00 0.00 0.00 4.40
652 707 2.291346 TGCTAGTAGTGTGGGAGTGCTA 60.291 50.000 0.00 0.00 0.00 3.49
653 708 2.359531 GCTAGTAGTGTGGGAGTGCTAG 59.640 54.545 0.00 0.00 41.17 3.42
654 709 2.606751 AGTAGTGTGGGAGTGCTAGT 57.393 50.000 0.00 0.00 0.00 2.57
655 710 2.890814 AGTAGTGTGGGAGTGCTAGTT 58.109 47.619 0.00 0.00 0.00 2.24
701 756 2.427753 GCATCCCCCATCTCGTCC 59.572 66.667 0.00 0.00 0.00 4.79
719 774 0.547712 CCTTGTCCTTCCCTCCCTCA 60.548 60.000 0.00 0.00 0.00 3.86
728 783 1.001641 CCCTCCCTCACTTGGCTTG 60.002 63.158 0.00 0.00 0.00 4.01
845 927 4.548513 CCCTCCCTCCCTCCCTCG 62.549 77.778 0.00 0.00 0.00 4.63
846 928 3.756783 CCTCCCTCCCTCCCTCGT 61.757 72.222 0.00 0.00 0.00 4.18
847 929 2.392816 CCTCCCTCCCTCCCTCGTA 61.393 68.421 0.00 0.00 0.00 3.43
860 942 2.027377 TCCCTCGTATCTCCGTATCTCC 60.027 54.545 0.00 0.00 0.00 3.71
885 980 4.028490 GGGTGGGTGATGCGGTGA 62.028 66.667 0.00 0.00 0.00 4.02
1260 1430 2.117156 CCCGATGCTCTGCCTTTGG 61.117 63.158 0.00 0.00 0.00 3.28
1297 1474 1.208293 CTTTTCCTCTCGGGGAGAAGG 59.792 57.143 6.42 1.51 44.45 3.46
1310 1487 3.181437 GGGGAGAAGGTGTTTTGTTCCTA 60.181 47.826 0.00 0.00 0.00 2.94
1356 1533 1.539776 CCTTTTTGTCTTGCGCGTGC 61.540 55.000 15.48 15.48 43.20 5.34
1575 1763 3.932710 TGCTTATGAGTTGTGACCGAATC 59.067 43.478 0.00 0.00 0.00 2.52
1616 1804 3.929610 GTCTTGTATGGTTGACTCAGAGC 59.070 47.826 0.00 0.00 0.00 4.09
1647 1835 1.999648 TGAGGAAACATTGCCTGCTT 58.000 45.000 0.00 0.00 33.84 3.91
1648 1836 3.153369 TGAGGAAACATTGCCTGCTTA 57.847 42.857 0.00 0.00 33.84 3.09
1696 1884 2.533266 TGGTTGACTCAGACTTGCTC 57.467 50.000 0.00 0.00 0.00 4.26
1722 1913 3.312697 GCTTGGCAGTAACTATTAGGTGC 59.687 47.826 0.00 0.00 0.00 5.01
1750 1941 1.532868 CTGGAAGTTCTCTTGCCGTTG 59.467 52.381 2.25 0.00 40.51 4.10
1863 2066 7.550551 GGAAATTACTGTTACCCTGTTACTACC 59.449 40.741 0.00 0.00 0.00 3.18
1886 2092 8.601845 ACCATTTTACAGTTTAATTTTCTGGC 57.398 30.769 8.36 0.00 34.02 4.85
1913 2119 7.118390 CCTGTCGATTCTTACCATATCATTTCC 59.882 40.741 0.00 0.00 0.00 3.13
1919 2125 2.645838 ACCATATCATTTCCGCTGCT 57.354 45.000 0.00 0.00 0.00 4.24
2050 2258 6.252967 TGTTGTGAGTTATATGCAACCAAG 57.747 37.500 0.00 0.00 38.75 3.61
2059 2267 2.806608 ATGCAACCAAGCTGTTTCAG 57.193 45.000 0.00 0.00 34.99 3.02
2142 2350 5.893897 AGAATTCCTTTGATCTGCTTGAC 57.106 39.130 0.65 0.00 0.00 3.18
2250 2458 8.143835 TCTTTTCTTTCCAAATCTGATTGTTCC 58.856 33.333 3.22 0.00 0.00 3.62
2262 2470 3.149196 TGATTGTTCCTTCTGCAGGTTC 58.851 45.455 15.13 0.00 44.37 3.62
2336 2544 6.981722 ACTCTTTGGTAAAAGCGATGAATTT 58.018 32.000 0.00 0.00 42.23 1.82
2360 2568 0.170561 CAGGTAGACCGTTGGAGTCG 59.829 60.000 0.00 0.00 42.08 4.18
3093 3301 7.071069 TGATGCATAGTTGATCAAGTAGGAT 57.929 36.000 29.83 23.29 31.67 3.24
3106 3314 2.588620 AGTAGGATAGGGAGCGTCTTG 58.411 52.381 0.00 0.00 0.00 3.02
3112 3320 4.464597 AGGATAGGGAGCGTCTTGAATATC 59.535 45.833 0.00 0.00 0.00 1.63
3115 3323 2.630580 AGGGAGCGTCTTGAATATCCTC 59.369 50.000 0.00 0.00 0.00 3.71
3123 3331 7.952671 AGCGTCTTGAATATCCTCTGTATTTA 58.047 34.615 0.00 0.00 0.00 1.40
3297 3505 8.356657 GTGATATGTCTCTTCTGTATAGCAACT 58.643 37.037 0.00 0.00 0.00 3.16
3339 3547 3.694043 TTAGTATGCTCTTGCCACACA 57.306 42.857 0.00 0.00 38.71 3.72
3352 3560 2.030363 TGCCACACATTTCGATTTCACC 60.030 45.455 0.00 0.00 0.00 4.02
3368 3576 5.772825 TTTCACCTTGCCATATAATCTGC 57.227 39.130 0.00 0.00 0.00 4.26
3418 3626 1.051812 ATGAGCTCCCGGATGTTAGG 58.948 55.000 12.15 0.00 0.00 2.69
3453 3661 2.886523 CAGTTGCCCATGTTCAAGAGAA 59.113 45.455 0.00 0.00 0.00 2.87
3468 3676 7.527457 GTTCAAGAGAACCTATTTTAACGCAT 58.473 34.615 0.00 0.00 46.68 4.73
3469 3677 7.681939 TCAAGAGAACCTATTTTAACGCATT 57.318 32.000 0.00 0.00 0.00 3.56
3470 3678 8.780846 TCAAGAGAACCTATTTTAACGCATTA 57.219 30.769 0.00 0.00 0.00 1.90
3471 3679 9.391006 TCAAGAGAACCTATTTTAACGCATTAT 57.609 29.630 0.00 0.00 0.00 1.28
3529 3749 3.084786 AGCATTTAGTCCCTTGCTGTTC 58.915 45.455 0.00 0.00 43.44 3.18
3537 3757 2.170607 GTCCCTTGCTGTTCTGCCTATA 59.829 50.000 0.00 0.00 0.00 1.31
3549 3769 6.301486 TGTTCTGCCTATATGCATTCTCATT 58.699 36.000 3.54 0.00 41.16 2.57
3550 3770 6.206048 TGTTCTGCCTATATGCATTCTCATTG 59.794 38.462 3.54 0.00 41.16 2.82
3551 3771 5.872963 TCTGCCTATATGCATTCTCATTGT 58.127 37.500 3.54 0.00 41.16 2.71
3552 3772 5.704053 TCTGCCTATATGCATTCTCATTGTG 59.296 40.000 3.54 0.00 41.16 3.33
3553 3773 5.623169 TGCCTATATGCATTCTCATTGTGA 58.377 37.500 3.54 0.00 36.04 3.58
3554 3774 6.063404 TGCCTATATGCATTCTCATTGTGAA 58.937 36.000 3.54 3.82 36.04 3.18
3555 3775 6.546772 TGCCTATATGCATTCTCATTGTGAAA 59.453 34.615 3.54 0.00 36.04 2.69
3556 3776 6.860023 GCCTATATGCATTCTCATTGTGAAAC 59.140 38.462 3.54 2.58 37.35 2.78
3625 3845 7.397476 TGATACTCCTGTCTAAGTGATCAAGTT 59.603 37.037 0.00 0.00 0.00 2.66
3744 3964 5.157770 TCTCCCCTATAATCCTGAGTTGT 57.842 43.478 0.00 0.00 0.00 3.32
3896 4116 2.762535 ATGTCTTGGAGGGTGTTACG 57.237 50.000 0.00 0.00 0.00 3.18
4032 4344 2.842457 TCGCTTGCTCTATTGCATCAT 58.158 42.857 0.00 0.00 42.96 2.45
4051 4363 5.918426 TCATGCACATGTTCATGGTTTAT 57.082 34.783 29.88 0.00 40.20 1.40
4055 4367 4.107622 GCACATGTTCATGGTTTATGCTC 58.892 43.478 15.71 0.00 36.70 4.26
4057 4369 3.378112 ACATGTTCATGGTTTATGCTCGG 59.622 43.478 15.71 0.00 36.70 4.63
4058 4370 3.342377 TGTTCATGGTTTATGCTCGGA 57.658 42.857 0.00 0.00 36.70 4.55
4066 4389 5.247507 TGGTTTATGCTCGGATTTCATTG 57.752 39.130 0.00 0.00 0.00 2.82
4112 4435 6.916360 TTTTGCAAGATTCTATTCCTTGGT 57.084 33.333 0.00 0.00 38.11 3.67
4165 4488 4.776837 TGAAAACCATGGAACCATAGCAAT 59.223 37.500 21.47 0.00 34.91 3.56
4176 4499 6.667414 TGGAACCATAGCAATTTTTCCTATGT 59.333 34.615 7.63 0.00 37.69 2.29
4235 4564 6.048732 TCCTTTGTGTCTATGACAATAGCA 57.951 37.500 1.73 0.00 44.49 3.49
4245 4574 4.519540 ATGACAATAGCAAACACCCAAC 57.480 40.909 0.00 0.00 0.00 3.77
4262 4591 6.013206 ACACCCAACCCTTAAAAATATTTCCC 60.013 38.462 0.10 0.00 0.00 3.97
4263 4592 6.214615 CACCCAACCCTTAAAAATATTTCCCT 59.785 38.462 0.10 0.00 0.00 4.20
4265 4594 7.037873 ACCCAACCCTTAAAAATATTTCCCTTC 60.038 37.037 0.10 0.00 0.00 3.46
4266 4595 7.335627 CCAACCCTTAAAAATATTTCCCTTCC 58.664 38.462 0.10 0.00 0.00 3.46
4270 4599 8.602424 ACCCTTAAAAATATTTCCCTTCCTTTG 58.398 33.333 0.10 0.00 0.00 2.77
4271 4600 8.602424 CCCTTAAAAATATTTCCCTTCCTTTGT 58.398 33.333 0.10 0.00 0.00 2.83
4272 4601 9.435688 CCTTAAAAATATTTCCCTTCCTTTGTG 57.564 33.333 0.10 0.00 0.00 3.33
4273 4602 9.996554 CTTAAAAATATTTCCCTTCCTTTGTGT 57.003 29.630 0.10 0.00 0.00 3.72
4274 4603 9.990360 TTAAAAATATTTCCCTTCCTTTGTGTC 57.010 29.630 0.10 0.00 0.00 3.67
4277 4654 7.939784 AATATTTCCCTTCCTTTGTGTCTAC 57.060 36.000 0.00 0.00 0.00 2.59
4284 4661 3.917329 TCCTTTGTGTCTACGACTCAG 57.083 47.619 0.00 0.00 37.36 3.35
4308 4685 4.750098 CGTATCATGACACCAATCCCTAAC 59.250 45.833 0.00 0.00 0.00 2.34
4360 4853 6.884295 CCTGTGAATGAAAAAGGTCCTATGTA 59.116 38.462 0.00 0.00 0.00 2.29
4398 4891 7.990917 TCTAACATTTGTGCTTACTTTGTCAA 58.009 30.769 0.00 0.00 0.00 3.18
4422 4915 1.995376 ATTGGGAAAGCAACCGAAGT 58.005 45.000 0.00 0.00 0.00 3.01
4431 4924 6.530181 GGGAAAGCAACCGAAGTATAAAATTG 59.470 38.462 0.00 0.00 0.00 2.32
4435 4928 6.768078 AGCAACCGAAGTATAAAATTGTACG 58.232 36.000 0.00 0.00 31.09 3.67
4439 4932 7.887996 ACCGAAGTATAAAATTGTACGTCAA 57.112 32.000 13.26 0.00 40.53 3.18
4487 4980 9.569122 TCCTTAAGCAGTTACAACTTTCTAAAT 57.431 29.630 0.00 0.00 37.08 1.40
4509 5002 5.756195 TTAGATGCATTGCCAGTTATCAC 57.244 39.130 6.12 0.00 0.00 3.06
4518 5011 2.172505 TGCCAGTTATCACGGAATGGAT 59.827 45.455 0.00 0.00 0.00 3.41
4551 5044 9.486497 AAGTGAGATATATGACATGTGTTCATC 57.514 33.333 1.15 0.00 31.15 2.92
4704 5198 6.594159 GCATAGTTTATCGGCTTATACCATGT 59.406 38.462 0.00 0.00 0.00 3.21
4712 5206 5.979993 TCGGCTTATACCATGTTCTTTGTA 58.020 37.500 0.00 0.00 0.00 2.41
4721 5215 2.163818 TGTTCTTTGTACTGCCTCCG 57.836 50.000 0.00 0.00 0.00 4.63
4735 5229 4.698780 ACTGCCTCCGTTTTTATTTACTCC 59.301 41.667 0.00 0.00 0.00 3.85
4736 5230 4.653868 TGCCTCCGTTTTTATTTACTCCA 58.346 39.130 0.00 0.00 0.00 3.86
4949 5444 3.466836 TCAGTCAAAGCTAATATGCGGG 58.533 45.455 0.00 0.00 38.13 6.13
4952 5447 2.548480 GTCAAAGCTAATATGCGGGGTC 59.452 50.000 0.00 0.00 38.13 4.46
4989 5485 6.160459 AGGGAGTATGTGATTTTACTGGGAAT 59.840 38.462 0.00 0.00 0.00 3.01
4990 5486 6.833933 GGGAGTATGTGATTTTACTGGGAATT 59.166 38.462 0.00 0.00 0.00 2.17
5186 5683 2.912956 TCTGTTCCCTATTCTGTGCCTT 59.087 45.455 0.00 0.00 0.00 4.35
5193 5690 3.118261 CCCTATTCTGTGCCTTCAGCTTA 60.118 47.826 0.00 0.00 44.23 3.09
5560 6057 1.136329 AGCTTTCCTGGGAAGAGGCA 61.136 55.000 19.17 0.00 35.38 4.75
5600 6097 2.224018 GCTCCATCTGCAAAACCAACAA 60.224 45.455 0.00 0.00 0.00 2.83
5652 6149 4.993584 AGAATATGATGTAAGCTGGCTTCG 59.006 41.667 11.28 0.00 37.47 3.79
6000 6499 0.040514 TTGCTCAAAATGGCGTCGTG 60.041 50.000 0.00 0.00 0.00 4.35
6080 6579 9.931210 GATCCAAAAAGGTAATACTATTTCACG 57.069 33.333 0.00 0.00 39.02 4.35
6168 6667 5.587443 TGATGATGGACTGCATACTGAAAAG 59.413 40.000 0.00 0.00 0.00 2.27
6386 6964 7.503521 TCTAATACTGTCTACTCATGAGCTG 57.496 40.000 22.83 14.97 0.00 4.24
6399 6977 7.744087 ACTCATGAGCTGTCTAATAGTCTAG 57.256 40.000 22.83 0.00 0.00 2.43
6581 7160 3.932710 ACACCAGTGCAATAATGTCGTAG 59.067 43.478 0.00 0.00 0.00 3.51
6673 7252 5.371115 TTGTGCTTAAATCAGTTGCTACC 57.629 39.130 0.00 0.00 0.00 3.18
6676 7255 5.106197 TGTGCTTAAATCAGTTGCTACCATG 60.106 40.000 0.00 0.00 0.00 3.66
6821 7400 1.928868 AGAAAGGACATTTGGGCAGG 58.071 50.000 0.00 0.00 0.00 4.85
6831 7410 0.758685 TTTGGGCAGGTTCACCTTGG 60.759 55.000 0.00 0.00 46.09 3.61
7424 8003 2.125188 GAGGAGGAGCAGCAGCAC 60.125 66.667 3.17 0.00 45.49 4.40
7457 8036 1.907739 GGTGAGCATGGTCAGCCTA 59.092 57.895 35.47 11.30 38.73 3.93
7460 8039 1.065854 GTGAGCATGGTCAGCCTACTT 60.066 52.381 27.11 0.00 35.27 2.24
7738 8317 0.836606 TGACCTGAGCTTGTTGACCA 59.163 50.000 0.00 0.00 0.00 4.02
7770 8349 4.146564 GTTAGTGGGTGGGTGTTTGTAAT 58.853 43.478 0.00 0.00 0.00 1.89
7803 8390 1.053424 TGTATGATCGGCTTACCCCC 58.947 55.000 0.00 0.00 0.00 5.40
7972 8559 1.675720 GCTGGCTGGTTGGTGTTGTT 61.676 55.000 0.00 0.00 0.00 2.83
8004 8591 4.043200 GCAACTCCAACGGGCTGC 62.043 66.667 0.00 0.00 0.00 5.25
8005 8592 2.281761 CAACTCCAACGGGCTGCT 60.282 61.111 0.00 0.00 0.00 4.24
8006 8593 2.281761 AACTCCAACGGGCTGCTG 60.282 61.111 0.00 0.00 0.00 4.41
8007 8594 2.818169 AACTCCAACGGGCTGCTGA 61.818 57.895 0.00 0.00 0.00 4.26
8008 8595 2.743928 CTCCAACGGGCTGCTGAC 60.744 66.667 0.00 0.00 0.00 3.51
8009 8596 4.329545 TCCAACGGGCTGCTGACC 62.330 66.667 5.14 5.14 38.25 4.02
8067 8655 0.822121 GGTCGCCCCTTTGTCTGTTT 60.822 55.000 0.00 0.00 0.00 2.83
8075 8663 3.016736 CCCTTTGTCTGTTTGTGTCTGT 58.983 45.455 0.00 0.00 0.00 3.41
8115 8703 4.292145 TGCGTCCAATGGGGCCAA 62.292 61.111 4.39 0.00 34.31 4.52
8139 8727 2.241722 CATTTTTGACATGTCCGCGTC 58.758 47.619 22.85 0.00 0.00 5.19
8149 8737 2.506217 TCCGCGTCGTCATTCAGC 60.506 61.111 4.92 0.00 0.00 4.26
8212 8816 4.704833 GGCTCTTCCCGTGCTGCA 62.705 66.667 0.00 0.00 32.84 4.41
8213 8817 3.123620 GCTCTTCCCGTGCTGCAG 61.124 66.667 10.11 10.11 0.00 4.41
8214 8818 3.123620 CTCTTCCCGTGCTGCAGC 61.124 66.667 31.89 31.89 42.50 5.25
8215 8819 3.602513 CTCTTCCCGTGCTGCAGCT 62.603 63.158 36.61 0.00 42.66 4.24
8216 8820 2.670934 CTTCCCGTGCTGCAGCTT 60.671 61.111 36.61 0.00 42.66 3.74
8217 8821 2.974489 CTTCCCGTGCTGCAGCTTG 61.974 63.158 36.61 27.53 42.66 4.01
8220 8824 4.400109 CCGTGCTGCAGCTTGCTG 62.400 66.667 36.61 21.23 45.31 4.41
8411 9015 4.475444 CCCGTGGCTCTCCCCCTA 62.475 72.222 0.00 0.00 0.00 3.53
8490 9108 2.363018 TGCAGTAGCTCTCGCCCT 60.363 61.111 0.00 0.00 42.74 5.19
8491 9109 2.105930 GCAGTAGCTCTCGCCCTG 59.894 66.667 0.00 0.00 38.17 4.45
8598 9492 0.390340 GCTCACGCACCTCAGATCAA 60.390 55.000 0.00 0.00 35.78 2.57
8609 9503 5.012561 GCACCTCAGATCAAGGACCTATAAT 59.987 44.000 18.28 0.00 37.35 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.915659 AACCAGTCCAGACGCCGA 60.916 61.111 0.00 0.00 36.20 5.54
64 65 4.855340 AGCGAGGAATTTTAGAATCCCAA 58.145 39.130 0.00 0.00 0.00 4.12
68 69 3.555956 TGCGAGCGAGGAATTTTAGAATC 59.444 43.478 0.00 0.00 0.00 2.52
231 246 2.151502 AGAAATGAGAGGAGGCGAGA 57.848 50.000 0.00 0.00 0.00 4.04
260 275 1.355796 TTCTATTGCCGACGTTGCCG 61.356 55.000 8.32 0.00 40.83 5.69
261 276 0.800012 TTTCTATTGCCGACGTTGCC 59.200 50.000 8.32 0.00 0.00 4.52
262 277 2.604969 TTTTCTATTGCCGACGTTGC 57.395 45.000 0.00 0.09 0.00 4.17
264 279 4.214545 TGTTCATTTTCTATTGCCGACGTT 59.785 37.500 0.00 0.00 0.00 3.99
318 333 2.103538 GCGCACATGCCAATCAGG 59.896 61.111 0.30 0.00 41.84 3.86
498 551 1.377612 GGGGACGGTAAAGCCAACT 59.622 57.895 0.00 0.00 36.97 3.16
499 552 0.537828 TTGGGGACGGTAAAGCCAAC 60.538 55.000 0.00 0.00 36.97 3.77
500 553 0.537828 GTTGGGGACGGTAAAGCCAA 60.538 55.000 0.00 0.00 36.97 4.52
501 554 1.073548 GTTGGGGACGGTAAAGCCA 59.926 57.895 0.00 0.00 36.97 4.75
502 555 1.676635 GGTTGGGGACGGTAAAGCC 60.677 63.158 0.00 0.00 0.00 4.35
503 556 1.676635 GGGTTGGGGACGGTAAAGC 60.677 63.158 0.00 0.00 0.00 3.51
505 558 1.463804 AGGGGTTGGGGACGGTAAA 60.464 57.895 0.00 0.00 0.00 2.01
506 559 1.919816 GAGGGGTTGGGGACGGTAA 60.920 63.158 0.00 0.00 0.00 2.85
507 560 2.284847 GAGGGGTTGGGGACGGTA 60.285 66.667 0.00 0.00 0.00 4.02
597 652 6.029346 TCCAAACTAGTAGTACGAAAAGGG 57.971 41.667 2.50 0.00 0.00 3.95
598 653 8.440833 CAAATCCAAACTAGTAGTACGAAAAGG 58.559 37.037 2.50 0.00 0.00 3.11
608 663 6.535508 GCACTACTCCAAATCCAAACTAGTAG 59.464 42.308 0.00 0.00 40.34 2.57
611 666 5.491982 AGCACTACTCCAAATCCAAACTAG 58.508 41.667 0.00 0.00 0.00 2.57
613 668 4.373156 AGCACTACTCCAAATCCAAACT 57.627 40.909 0.00 0.00 0.00 2.66
614 669 5.246307 ACTAGCACTACTCCAAATCCAAAC 58.754 41.667 0.00 0.00 0.00 2.93
615 670 5.499004 ACTAGCACTACTCCAAATCCAAA 57.501 39.130 0.00 0.00 0.00 3.28
616 671 5.720041 ACTACTAGCACTACTCCAAATCCAA 59.280 40.000 0.00 0.00 0.00 3.53
618 673 5.127356 ACACTACTAGCACTACTCCAAATCC 59.873 44.000 0.00 0.00 0.00 3.01
620 675 5.105310 CCACACTACTAGCACTACTCCAAAT 60.105 44.000 0.00 0.00 0.00 2.32
621 676 4.219944 CCACACTACTAGCACTACTCCAAA 59.780 45.833 0.00 0.00 0.00 3.28
622 677 3.762288 CCACACTACTAGCACTACTCCAA 59.238 47.826 0.00 0.00 0.00 3.53
624 679 2.688958 CCCACACTACTAGCACTACTCC 59.311 54.545 0.00 0.00 0.00 3.85
626 681 3.010361 ACTCCCACACTACTAGCACTACT 59.990 47.826 0.00 0.00 0.00 2.57
627 682 3.128938 CACTCCCACACTACTAGCACTAC 59.871 52.174 0.00 0.00 0.00 2.73
628 683 3.353557 CACTCCCACACTACTAGCACTA 58.646 50.000 0.00 0.00 0.00 2.74
629 684 2.171840 CACTCCCACACTACTAGCACT 58.828 52.381 0.00 0.00 0.00 4.40
630 685 1.404315 GCACTCCCACACTACTAGCAC 60.404 57.143 0.00 0.00 0.00 4.40
631 686 0.895530 GCACTCCCACACTACTAGCA 59.104 55.000 0.00 0.00 0.00 3.49
632 687 1.187087 AGCACTCCCACACTACTAGC 58.813 55.000 0.00 0.00 0.00 3.42
633 688 3.622630 ACTAGCACTCCCACACTACTAG 58.377 50.000 0.00 0.00 33.50 2.57
634 689 3.733883 ACTAGCACTCCCACACTACTA 57.266 47.619 0.00 0.00 0.00 1.82
635 690 2.606751 ACTAGCACTCCCACACTACT 57.393 50.000 0.00 0.00 0.00 2.57
636 691 3.679824 AAACTAGCACTCCCACACTAC 57.320 47.619 0.00 0.00 0.00 2.73
637 692 4.219944 CAGTAAACTAGCACTCCCACACTA 59.780 45.833 0.00 0.00 0.00 2.74
638 693 3.006967 CAGTAAACTAGCACTCCCACACT 59.993 47.826 0.00 0.00 0.00 3.55
639 694 3.326747 CAGTAAACTAGCACTCCCACAC 58.673 50.000 0.00 0.00 0.00 3.82
640 695 2.289444 GCAGTAAACTAGCACTCCCACA 60.289 50.000 0.00 0.00 0.00 4.17
641 696 2.028020 AGCAGTAAACTAGCACTCCCAC 60.028 50.000 0.00 0.00 0.00 4.61
642 697 2.233922 GAGCAGTAAACTAGCACTCCCA 59.766 50.000 0.00 0.00 0.00 4.37
643 698 2.735762 CGAGCAGTAAACTAGCACTCCC 60.736 54.545 0.00 0.00 0.00 4.30
644 699 2.531206 CGAGCAGTAAACTAGCACTCC 58.469 52.381 0.00 0.00 0.00 3.85
645 700 1.921230 GCGAGCAGTAAACTAGCACTC 59.079 52.381 0.00 0.00 36.01 3.51
646 701 1.272490 TGCGAGCAGTAAACTAGCACT 59.728 47.619 0.00 0.00 40.24 4.40
647 702 1.656095 CTGCGAGCAGTAAACTAGCAC 59.344 52.381 16.29 0.00 40.24 4.40
648 703 1.404181 CCTGCGAGCAGTAAACTAGCA 60.404 52.381 21.73 0.00 42.41 3.49
649 704 1.281899 CCTGCGAGCAGTAAACTAGC 58.718 55.000 21.73 0.00 42.15 3.42
650 705 1.281899 GCCTGCGAGCAGTAAACTAG 58.718 55.000 21.73 7.46 42.15 2.57
651 706 0.606096 TGCCTGCGAGCAGTAAACTA 59.394 50.000 21.73 1.26 42.15 2.24
652 707 1.371183 TGCCTGCGAGCAGTAAACT 59.629 52.632 21.73 0.00 42.15 2.66
653 708 3.966215 TGCCTGCGAGCAGTAAAC 58.034 55.556 21.73 10.12 42.15 2.01
677 732 4.290622 ATGGGGGATGCCGGATGC 62.291 66.667 5.05 0.56 41.77 3.91
678 733 2.034687 GATGGGGGATGCCGGATG 59.965 66.667 5.05 0.00 0.00 3.51
679 734 2.121781 AGATGGGGGATGCCGGAT 60.122 61.111 5.05 0.00 0.00 4.18
701 756 0.615850 GTGAGGGAGGGAAGGACAAG 59.384 60.000 0.00 0.00 0.00 3.16
719 774 3.064324 GATGCGGGCAAGCCAAGT 61.064 61.111 13.87 0.00 37.98 3.16
750 815 4.129737 CGATCGGTGGCGACTGGT 62.130 66.667 7.38 0.00 0.00 4.00
863 945 4.796495 GCATCACCCACCCCCGAC 62.796 72.222 0.00 0.00 0.00 4.79
885 980 0.900647 AAGCAGAGTACACCTCGCCT 60.901 55.000 0.00 0.00 45.44 5.52
895 990 2.874457 GCCGAAAAGGGAAAGCAGAGTA 60.874 50.000 0.00 0.00 41.48 2.59
1141 1248 2.257541 TAGCAGGAAGGGGAGGGGAG 62.258 65.000 0.00 0.00 0.00 4.30
1142 1249 2.261293 TAGCAGGAAGGGGAGGGGA 61.261 63.158 0.00 0.00 0.00 4.81
1143 1250 2.073101 GTAGCAGGAAGGGGAGGGG 61.073 68.421 0.00 0.00 0.00 4.79
1144 1251 2.073101 GGTAGCAGGAAGGGGAGGG 61.073 68.421 0.00 0.00 0.00 4.30
1145 1252 1.306997 TGGTAGCAGGAAGGGGAGG 60.307 63.158 0.00 0.00 0.00 4.30
1146 1253 1.627297 GGTGGTAGCAGGAAGGGGAG 61.627 65.000 0.00 0.00 0.00 4.30
1147 1254 1.615424 GGTGGTAGCAGGAAGGGGA 60.615 63.158 0.00 0.00 0.00 4.81
1243 1413 3.506108 CCAAAGGCAGAGCATCGG 58.494 61.111 0.00 0.00 42.67 4.18
1297 1474 2.356695 ACCGCAACTAGGAACAAAACAC 59.643 45.455 0.00 0.00 0.00 3.32
1356 1533 4.266976 CACTTTTCTGAAAAACTGCTGCTG 59.733 41.667 15.67 4.89 31.23 4.41
1381 1561 4.187056 GCTACAGCCGAGTCAACC 57.813 61.111 0.00 0.00 34.31 3.77
1575 1763 3.243771 AGACACAGAGGTGACTTTTACCG 60.244 47.826 1.30 0.00 45.53 4.02
1616 1804 1.000938 GTTTCCTCAAGCAAGCACCAG 60.001 52.381 0.00 0.00 0.00 4.00
1696 1884 4.576463 CCTAATAGTTACTGCCAAGCAAGG 59.424 45.833 0.00 0.00 38.41 3.61
1722 1913 3.742433 AGAGAACTTCCAGTGTCACAG 57.258 47.619 5.62 0.00 0.00 3.66
1746 1937 3.536158 ACATGTCATCGAAAACCAACG 57.464 42.857 0.00 0.00 0.00 4.10
1750 1941 8.665685 ACTAGATTAAACATGTCATCGAAAACC 58.334 33.333 0.00 0.00 0.00 3.27
1804 2007 9.346725 GCAGGAAAAACAATCTTCAAATACTAG 57.653 33.333 0.00 0.00 0.00 2.57
1805 2008 8.855110 TGCAGGAAAAACAATCTTCAAATACTA 58.145 29.630 0.00 0.00 0.00 1.82
1806 2009 7.725251 TGCAGGAAAAACAATCTTCAAATACT 58.275 30.769 0.00 0.00 0.00 2.12
1863 2066 7.877612 AGGGCCAGAAAATTAAACTGTAAAATG 59.122 33.333 6.18 0.00 0.00 2.32
1886 2092 5.468540 TGATATGGTAAGAATCGACAGGG 57.531 43.478 0.00 0.00 0.00 4.45
1913 2119 3.123620 GCCAACCTGAGAGCAGCG 61.124 66.667 0.00 0.00 40.91 5.18
1919 2125 1.289066 CTCGAACGCCAACCTGAGA 59.711 57.895 0.00 0.00 0.00 3.27
2050 2258 6.587608 CCTTGGAATTATTGTTCTGAAACAGC 59.412 38.462 0.00 0.00 45.72 4.40
2059 2267 3.384789 GGAGCCCCTTGGAATTATTGTTC 59.615 47.826 0.00 0.00 0.00 3.18
2142 2350 1.699656 CGCATTGAACTCCTCCGCTG 61.700 60.000 0.00 0.00 0.00 5.18
2250 2458 2.189594 TGACATGGAACCTGCAGAAG 57.810 50.000 17.39 1.02 0.00 2.85
2262 2470 1.542915 CTTTGGAGCCACTTGACATGG 59.457 52.381 0.00 0.00 40.50 3.66
2336 2544 0.250553 CCAACGGTCTACCTGGCAAA 60.251 55.000 0.00 0.00 0.00 3.68
2360 2568 0.249911 AATCGAGCATAAGGGACGGC 60.250 55.000 0.00 0.00 0.00 5.68
3037 3245 8.972262 TTGCACGTAAATAATTAAAGCATCAA 57.028 26.923 0.00 0.00 29.89 2.57
3053 3261 5.302357 TGCATCATGTAATTTGCACGTAA 57.698 34.783 0.00 0.00 37.80 3.18
3093 3301 3.827302 GAGGATATTCAAGACGCTCCCTA 59.173 47.826 0.00 0.00 0.00 3.53
3123 3331 7.768120 ACACAACACAATATCCACAACAAAAAT 59.232 29.630 0.00 0.00 0.00 1.82
3308 3516 9.007901 GGCAAGAGCATACTAAATTATGAAGAT 57.992 33.333 0.00 0.00 44.61 2.40
3329 3537 3.670055 GTGAAATCGAAATGTGTGGCAAG 59.330 43.478 0.00 0.00 0.00 4.01
3339 3547 7.581213 TTATATGGCAAGGTGAAATCGAAAT 57.419 32.000 0.00 0.00 0.00 2.17
3352 3560 9.917129 TTTTATTCATGCAGATTATATGGCAAG 57.083 29.630 0.00 0.00 40.02 4.01
3418 3626 2.730550 CAACTGTGCTTCCCCAAATC 57.269 50.000 0.00 0.00 0.00 2.17
3537 3757 6.275494 TGATGTTTCACAATGAGAATGCAT 57.725 33.333 0.00 0.00 0.00 3.96
3563 3783 9.812347 TGATGTTTCCATTCTAAATAGGCATAT 57.188 29.630 0.00 0.00 0.00 1.78
3564 3784 9.812347 ATGATGTTTCCATTCTAAATAGGCATA 57.188 29.630 0.00 0.00 0.00 3.14
3565 3785 8.716674 ATGATGTTTCCATTCTAAATAGGCAT 57.283 30.769 0.00 0.00 0.00 4.40
3566 3786 8.537728 AATGATGTTTCCATTCTAAATAGGCA 57.462 30.769 0.00 0.00 28.89 4.75
3615 3835 6.863126 CCATGAAACAGGTTTAACTTGATCAC 59.137 38.462 14.04 1.91 31.81 3.06
3625 3845 7.469456 GCACTTTCTAACCATGAAACAGGTTTA 60.469 37.037 1.84 0.00 45.46 2.01
3722 3942 5.157770 ACAACTCAGGATTATAGGGGAGA 57.842 43.478 0.00 0.00 0.00 3.71
3744 3964 4.537945 AGGCCTACATAGAGTACCTCAA 57.462 45.455 1.29 0.00 32.06 3.02
3770 3990 0.107312 CTGGCTGAGAGATTGGTGGG 60.107 60.000 0.00 0.00 0.00 4.61
3830 4050 5.159209 CAGAATCTGAACTGAAAATGCCAC 58.841 41.667 3.77 0.00 36.38 5.01
3896 4116 2.917933 TGTAAGGACTGTATGCATGGC 58.082 47.619 10.16 2.61 0.00 4.40
4032 4344 3.510753 AGCATAAACCATGAACATGTGCA 59.489 39.130 9.52 9.52 37.90 4.57
4051 4363 5.393352 CCTTTGAATCAATGAAATCCGAGCA 60.393 40.000 10.03 0.00 0.00 4.26
4055 4367 7.223387 GGAATTCCTTTGAATCAATGAAATCCG 59.777 37.037 17.73 2.49 40.34 4.18
4057 4369 9.609346 ATGGAATTCCTTTGAATCAATGAAATC 57.391 29.630 24.73 11.16 40.34 2.17
4176 4499 7.284261 TCCTTCGGAATTGCATGTGAATTATTA 59.716 33.333 0.00 0.00 0.00 0.98
4213 4536 6.741992 TTGCTATTGTCATAGACACAAAGG 57.258 37.500 0.00 0.00 42.60 3.11
4214 4537 7.535258 GTGTTTGCTATTGTCATAGACACAAAG 59.465 37.037 11.48 6.23 42.60 2.77
4235 4564 7.940137 GGAAATATTTTTAAGGGTTGGGTGTTT 59.060 33.333 1.43 0.00 0.00 2.83
4245 4574 8.602424 ACAAAGGAAGGGAAATATTTTTAAGGG 58.398 33.333 1.43 0.00 0.00 3.95
4273 4602 3.247886 GTCATGATACGCTGAGTCGTAGA 59.752 47.826 12.86 4.52 46.32 2.59
4274 4603 3.002348 TGTCATGATACGCTGAGTCGTAG 59.998 47.826 12.86 2.72 46.32 3.51
4277 4654 2.112522 GTGTCATGATACGCTGAGTCG 58.887 52.381 6.86 0.00 0.00 4.18
4284 4661 1.873591 GGGATTGGTGTCATGATACGC 59.126 52.381 15.41 9.61 0.00 4.42
4328 4821 9.136323 GGACCTTTTTCATTCACAGGATTATAT 57.864 33.333 0.00 0.00 0.00 0.86
4375 4868 9.593134 AAATTGACAAAGTAAGCACAAATGTTA 57.407 25.926 0.00 0.00 0.00 2.41
4395 4888 5.011125 TCGGTTGCTTTCCCAATAAAATTGA 59.989 36.000 1.23 0.00 0.00 2.57
4398 4891 5.011635 ACTTCGGTTGCTTTCCCAATAAAAT 59.988 36.000 0.00 0.00 0.00 1.82
4443 4936 9.521503 GCTTAAGGAGATTCATAATTTGTTTCC 57.478 33.333 4.29 0.00 0.00 3.13
4446 4939 9.247861 ACTGCTTAAGGAGATTCATAATTTGTT 57.752 29.630 28.42 0.00 36.93 2.83
4474 4967 7.761249 GGCAATGCATCTAATTTAGAAAGTTGT 59.239 33.333 7.79 0.00 38.50 3.32
4487 4980 4.273235 CGTGATAACTGGCAATGCATCTAA 59.727 41.667 7.79 0.00 0.00 2.10
4509 5002 3.270027 TCACTTGCACTTATCCATTCCG 58.730 45.455 0.00 0.00 0.00 4.30
4518 5011 8.424133 ACATGTCATATATCTCACTTGCACTTA 58.576 33.333 0.00 0.00 0.00 2.24
4587 5080 6.154203 TGTTGCTGGACATGACAATTTAAA 57.846 33.333 0.00 0.00 0.00 1.52
4589 5082 4.321156 GCTGTTGCTGGACATGACAATTTA 60.321 41.667 0.00 0.00 36.03 1.40
4685 5178 7.554835 ACAAAGAACATGGTATAAGCCGATAAA 59.445 33.333 0.00 0.00 0.00 1.40
4686 5179 7.051623 ACAAAGAACATGGTATAAGCCGATAA 58.948 34.615 0.00 0.00 0.00 1.75
4688 5181 5.437060 ACAAAGAACATGGTATAAGCCGAT 58.563 37.500 0.00 0.00 0.00 4.18
4689 5182 4.839121 ACAAAGAACATGGTATAAGCCGA 58.161 39.130 0.00 0.00 0.00 5.54
4690 5183 5.815740 AGTACAAAGAACATGGTATAAGCCG 59.184 40.000 0.00 0.00 0.00 5.52
4704 5198 2.922740 AACGGAGGCAGTACAAAGAA 57.077 45.000 0.00 0.00 0.00 2.52
4712 5206 4.698780 GGAGTAAATAAAAACGGAGGCAGT 59.301 41.667 0.00 0.00 0.00 4.40
4758 5253 8.872845 CAAACTTGTTGAAAGCTCATAAAGTTT 58.127 29.630 15.90 15.90 46.15 2.66
4767 5262 5.751243 TCCTACAAACTTGTTGAAAGCTC 57.249 39.130 0.00 0.00 42.35 4.09
4949 5444 3.682696 ACTCCCTCCGTTTTTATTGACC 58.317 45.455 0.00 0.00 0.00 4.02
4952 5447 5.878116 TCACATACTCCCTCCGTTTTTATTG 59.122 40.000 0.00 0.00 0.00 1.90
5019 5515 9.408648 CCAGTACATATAAAAATCTTCCCAGTT 57.591 33.333 0.00 0.00 0.00 3.16
5512 6009 0.321996 GGGCCTCCTCGTTATCCATC 59.678 60.000 0.84 0.00 0.00 3.51
5560 6057 0.532862 CAGGACGCAACAACTCCTGT 60.533 55.000 7.61 0.00 44.28 4.00
5600 6097 8.991783 AATTCATAGTCCTCAATCATCACAAT 57.008 30.769 0.00 0.00 0.00 2.71
5652 6149 1.583054 AGTGCTGGAACGTGAAGAAC 58.417 50.000 0.00 0.00 0.00 3.01
5698 6195 5.824624 TGCTGAGAATGAAGAGTTGTCTTTT 59.175 36.000 0.00 0.00 43.50 2.27
5699 6196 5.371526 TGCTGAGAATGAAGAGTTGTCTTT 58.628 37.500 0.00 0.00 43.50 2.52
6000 6499 5.300286 AGGCAATAATGACATTAAGAGGCAC 59.700 40.000 21.97 13.42 36.86 5.01
6080 6579 7.539710 GGAATAAAAATAGGTTCCGTCACAAAC 59.460 37.037 0.00 0.00 31.73 2.93
6168 6667 5.048434 ACCAGAATCAGTCAAAAGCTTAAGC 60.048 40.000 20.09 20.09 42.49 3.09
6462 7040 6.327934 CAATAGAGAATTGTTTCAAGGCTGG 58.672 40.000 0.00 0.00 40.19 4.85
6560 7138 3.242413 GCTACGACATTATTGCACTGGTG 60.242 47.826 0.00 0.00 0.00 4.17
6577 7156 4.175787 ACACTAACAAAGAGAGGCTACG 57.824 45.455 0.00 0.00 0.00 3.51
6581 7160 5.948992 ATGAAACACTAACAAAGAGAGGC 57.051 39.130 0.00 0.00 0.00 4.70
6625 7204 3.671702 GCTAAGCAGAATGTGAAAGCACC 60.672 47.826 0.00 0.00 44.51 5.01
6673 7252 1.211969 GCAGGAACAGCTGCACATG 59.788 57.895 15.27 16.39 45.11 3.21
6766 7345 1.483415 TGTACTCTTGTTATCGGGGCC 59.517 52.381 0.00 0.00 0.00 5.80
6771 7350 9.133627 CATGGATATCTTGTACTCTTGTTATCG 57.866 37.037 2.05 0.00 0.00 2.92
6821 7400 6.264518 TCATTTCTACTTTTCCCAAGGTGAAC 59.735 38.462 0.00 0.00 0.00 3.18
7457 8036 2.049433 CGGTTCGCGACCTCAAGT 60.049 61.111 9.15 0.00 46.92 3.16
7738 8317 1.377202 CCCACTAACACAGGCGCAT 60.377 57.895 10.83 0.00 0.00 4.73
7770 8349 5.504830 CCGATCATACACACACACAAACAAA 60.505 40.000 0.00 0.00 0.00 2.83
7825 8412 3.814842 TGATCTTCACATCAAAACGCACT 59.185 39.130 0.00 0.00 29.41 4.40
7972 8559 1.916273 TTGCTCTTAGGCGTGGGGA 60.916 57.895 0.00 0.00 34.52 4.81
8004 8591 1.959226 CGGTGTCCGTTTGGGTCAG 60.959 63.158 0.00 0.00 42.73 3.51
8005 8592 2.109387 CGGTGTCCGTTTGGGTCA 59.891 61.111 0.00 0.00 42.73 4.02
8010 8597 7.666525 AGGAAACAAAATCGGTGTCCGTTTG 62.667 44.000 16.76 16.76 45.61 2.93
8011 8598 5.701569 AGGAAACAAAATCGGTGTCCGTTT 61.702 41.667 8.03 3.63 45.61 3.60
8012 8599 4.244828 AGGAAACAAAATCGGTGTCCGTT 61.245 43.478 8.03 0.00 45.61 4.44
8013 8600 2.747135 AGGAAACAAAATCGGTGTCCGT 60.747 45.455 8.03 0.00 45.61 4.69
8014 8601 1.877443 AGGAAACAAAATCGGTGTCCG 59.123 47.619 1.45 1.45 45.61 4.79
8015 8602 4.316205 AAAGGAAACAAAATCGGTGTCC 57.684 40.909 0.00 0.00 42.07 4.02
8028 8615 4.827692 ACCCAAACAGACAAAAAGGAAAC 58.172 39.130 0.00 0.00 0.00 2.78
8031 8618 2.685897 CGACCCAAACAGACAAAAAGGA 59.314 45.455 0.00 0.00 0.00 3.36
8032 8619 2.798145 GCGACCCAAACAGACAAAAAGG 60.798 50.000 0.00 0.00 0.00 3.11
8107 8695 0.533755 CAAAAATGCGTTTGGCCCCA 60.534 50.000 4.29 0.00 42.61 4.96
8109 8697 0.865111 GTCAAAAATGCGTTTGGCCC 59.135 50.000 4.29 0.00 42.61 5.80
8112 8700 3.184178 GGACATGTCAAAAATGCGTTTGG 59.816 43.478 26.47 0.85 38.72 3.28
8115 8703 2.660490 CGGACATGTCAAAAATGCGTT 58.340 42.857 26.47 0.00 0.00 4.84
8196 8800 3.123620 CTGCAGCACGGGAAGAGC 61.124 66.667 0.00 0.00 36.67 4.09
8198 8802 3.182590 AAGCTGCAGCACGGGAAGA 62.183 57.895 38.24 0.00 45.16 2.87
8200 8804 2.979676 CAAGCTGCAGCACGGGAA 60.980 61.111 38.24 0.00 45.16 3.97
8462 9076 3.729965 CTACTGCAGCCCCAGCGAG 62.730 68.421 15.27 0.00 46.67 5.03
8463 9077 3.774528 CTACTGCAGCCCCAGCGA 61.775 66.667 15.27 0.00 46.67 4.93
8587 9205 8.013667 ACTTATTATAGGTCCTTGATCTGAGGT 58.986 37.037 13.28 0.89 35.71 3.85


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

AutoCloner maintained by Alex Coulton.