Multiple sequence alignment - TraesCS7D01G174300

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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 TraesCS7D01G174300 chr7D 100.000 4190 0 0 1 4190 126680685 126684874 0.000000e+00 7738.0
1 TraesCS7D01G174300 chr7D 95.200 2125 93 5 1073 3188 126507329 126505205 0.000000e+00 3350.0
2 TraesCS7D01G174300 chr7D 92.411 817 55 3 1411 2227 88363289 88362480 0.000000e+00 1158.0
3 TraesCS7D01G174300 chr7D 91.791 536 17 11 64 576 126511652 126511121 0.000000e+00 721.0
4 TraesCS7D01G174300 chr7D 92.627 217 16 0 3279 3495 218082390 218082606 3.150000e-81 313.0
5 TraesCS7D01G174300 chr7D 92.093 215 17 0 3281 3495 315667216 315667430 1.890000e-78 303.0
6 TraesCS7D01G174300 chr7D 91.743 218 18 0 3281 3498 340970524 340970307 1.890000e-78 303.0
7 TraesCS7D01G174300 chr7D 91.379 174 12 3 3530 3701 126504976 126504804 7.000000e-58 235.0
8 TraesCS7D01G174300 chr7D 92.473 93 3 3 731 823 126508049 126507961 3.400000e-26 130.0
9 TraesCS7D01G174300 chr7B 94.337 2578 114 20 731 3291 87174637 87172075 0.000000e+00 3923.0
10 TraesCS7D01G174300 chr7B 93.464 2494 125 19 736 3203 88244996 88247477 0.000000e+00 3668.0
11 TraesCS7D01G174300 chr7B 86.656 637 76 9 3559 4190 87170835 87170203 0.000000e+00 697.0
12 TraesCS7D01G174300 chr7B 84.571 687 64 14 3511 4190 88247580 88248231 0.000000e+00 643.0
13 TraesCS7D01G174300 chr7B 89.562 297 19 7 64 358 87176980 87176694 2.380000e-97 366.0
14 TraesCS7D01G174300 chr7B 89.542 153 7 4 433 576 87176693 87176541 7.150000e-43 185.0
15 TraesCS7D01G174300 chr7B 100.000 48 0 0 3520 3567 87171969 87171922 5.770000e-14 89.8
16 TraesCS7D01G174300 chr7B 100.000 29 0 0 615 643 87174819 87174791 2.000000e-03 54.7
17 TraesCS7D01G174300 chr7A 95.236 1952 81 4 1251 3190 127607553 127609504 0.000000e+00 3079.0
18 TraesCS7D01G174300 chr7A 93.137 510 16 7 740 1246 127607010 127607503 0.000000e+00 730.0
19 TraesCS7D01G174300 chr7A 87.539 321 25 11 62 378 127603088 127603397 1.430000e-94 357.0
20 TraesCS7D01G174300 chr7A 82.426 404 50 4 3515 3917 127636380 127636763 2.410000e-87 333.0
21 TraesCS7D01G174300 chr7A 100.000 28 0 0 3255 3282 127609584 127609611 8.000000e-03 52.8
22 TraesCS7D01G174300 chr4D 93.635 817 43 4 1411 2227 33240758 33241565 0.000000e+00 1212.0
23 TraesCS7D01G174300 chr4D 73.063 1136 273 30 2065 3188 122258737 122257623 5.120000e-99 372.0
24 TraesCS7D01G174300 chr4D 83.756 197 23 7 1023 1210 122303610 122303414 1.200000e-40 178.0
25 TraesCS7D01G174300 chr5D 93.390 817 45 4 1411 2227 457999143 457998336 0.000000e+00 1201.0
26 TraesCS7D01G174300 chr5D 93.636 220 14 0 3279 3498 334254196 334254415 3.120000e-86 329.0
27 TraesCS7D01G174300 chr5D 91.705 217 18 0 3282 3498 88270668 88270452 6.810000e-78 302.0
28 TraesCS7D01G174300 chr3D 93.146 817 49 4 1411 2227 538375321 538374512 0.000000e+00 1192.0
29 TraesCS7D01G174300 chr3D 92.656 817 53 3 1411 2227 26470223 26471032 0.000000e+00 1170.0
30 TraesCS7D01G174300 chr4A 73.263 1137 269 32 2065 3188 448104143 448105257 2.360000e-102 383.0
31 TraesCS7D01G174300 chr4A 84.848 198 21 6 1023 1211 447777086 447777283 1.540000e-44 191.0
32 TraesCS7D01G174300 chr6D 93.151 219 14 1 3278 3495 151509103 151509321 1.880000e-83 320.0
33 TraesCS7D01G174300 chr2D 92.166 217 17 0 3282 3498 155616774 155616558 1.460000e-79 307.0
34 TraesCS7D01G174300 chr1A 91.743 218 16 2 3282 3498 134193736 134193520 6.810000e-78 302.0
35 TraesCS7D01G174300 chr2A 90.783 217 20 0 3282 3498 716521555 716521339 1.470000e-74 291.0
36 TraesCS7D01G174300 chr4B 86.709 158 18 1 1062 1219 186609259 186609105 5.570000e-39 172.0
37 TraesCS7D01G174300 chr3B 91.489 94 8 0 1072 1165 71265548 71265455 3.400000e-26 130.0


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 TraesCS7D01G174300 chr7D 126680685 126684874 4189 False 7738.000000 7738 100.00000 1 4190 1 chr7D.!!$F1 4189
1 TraesCS7D01G174300 chr7D 88362480 88363289 809 True 1158.000000 1158 92.41100 1411 2227 1 chr7D.!!$R1 816
2 TraesCS7D01G174300 chr7D 126504804 126511652 6848 True 1109.000000 3350 92.71075 64 3701 4 chr7D.!!$R3 3637
3 TraesCS7D01G174300 chr7B 88244996 88248231 3235 False 2155.500000 3668 89.01750 736 4190 2 chr7B.!!$F1 3454
4 TraesCS7D01G174300 chr7B 87170203 87176980 6777 True 885.916667 3923 93.34950 64 4190 6 chr7B.!!$R1 4126
5 TraesCS7D01G174300 chr7A 127603088 127609611 6523 False 1054.700000 3079 93.97800 62 3282 4 chr7A.!!$F2 3220
6 TraesCS7D01G174300 chr4D 33240758 33241565 807 False 1212.000000 1212 93.63500 1411 2227 1 chr4D.!!$F1 816
7 TraesCS7D01G174300 chr4D 122257623 122258737 1114 True 372.000000 372 73.06300 2065 3188 1 chr4D.!!$R1 1123
8 TraesCS7D01G174300 chr5D 457998336 457999143 807 True 1201.000000 1201 93.39000 1411 2227 1 chr5D.!!$R2 816
9 TraesCS7D01G174300 chr3D 538374512 538375321 809 True 1192.000000 1192 93.14600 1411 2227 1 chr3D.!!$R1 816
10 TraesCS7D01G174300 chr3D 26470223 26471032 809 False 1170.000000 1170 92.65600 1411 2227 1 chr3D.!!$F1 816
11 TraesCS7D01G174300 chr4A 448104143 448105257 1114 False 383.000000 383 73.26300 2065 3188 1 chr4A.!!$F2 1123

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
469 525 0.034337 TTGACCCGTTCTGTACTGCC 59.966 55.0 0.00 0.0 0.00 4.85 F
966 5722 0.314302 ACTCGTCGCACTTAGCACTT 59.686 50.0 0.00 0.0 46.13 3.16 F
2001 7199 0.108585 ACAGCGAGGCCAAGAAGAAA 59.891 50.0 5.01 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 6944 0.037232 CCACCTCGTCCTTCTTCACC 60.037 60.0 0.0 0.0 0.0 4.02 R
2021 7219 0.108567 GACCGCCTCACTCTTCTTCC 60.109 60.0 0.0 0.0 0.0 3.46 R
3488 8796 0.106894 CCCTCCTTCCGGTCTAATGC 59.893 60.0 0.0 0.0 0.0 3.56 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
18 19 3.243128 GTAAGGTCATGGCACCGTT 57.757 52.632 0.00 0.00 41.90 4.44
19 20 1.530323 GTAAGGTCATGGCACCGTTT 58.470 50.000 0.00 0.00 41.90 3.60
20 21 1.199097 GTAAGGTCATGGCACCGTTTG 59.801 52.381 0.00 0.00 41.90 2.93
21 22 0.179004 AAGGTCATGGCACCGTTTGA 60.179 50.000 0.00 0.00 41.90 2.69
22 23 0.038166 AGGTCATGGCACCGTTTGAT 59.962 50.000 0.00 0.00 41.90 2.57
23 24 0.887933 GGTCATGGCACCGTTTGATT 59.112 50.000 0.00 0.00 0.00 2.57
24 25 1.402720 GGTCATGGCACCGTTTGATTG 60.403 52.381 0.00 0.00 0.00 2.67
25 26 0.887247 TCATGGCACCGTTTGATTGG 59.113 50.000 0.00 0.00 0.00 3.16
26 27 0.737019 CATGGCACCGTTTGATTGGC 60.737 55.000 0.00 0.00 36.39 4.52
27 28 1.887344 ATGGCACCGTTTGATTGGCC 61.887 55.000 0.00 0.00 41.70 5.36
28 29 2.569354 GGCACCGTTTGATTGGCCA 61.569 57.895 0.00 0.00 41.02 5.36
29 30 1.372872 GCACCGTTTGATTGGCCAC 60.373 57.895 3.88 0.00 0.00 5.01
30 31 2.037053 CACCGTTTGATTGGCCACA 58.963 52.632 3.88 0.00 0.00 4.17
31 32 0.318614 CACCGTTTGATTGGCCACAC 60.319 55.000 3.88 2.55 0.00 3.82
32 33 1.288752 CCGTTTGATTGGCCACACC 59.711 57.895 3.88 0.00 39.84 4.16
33 34 1.288752 CGTTTGATTGGCCACACCC 59.711 57.895 3.88 0.00 37.83 4.61
34 35 1.459455 CGTTTGATTGGCCACACCCA 61.459 55.000 3.88 0.00 37.83 4.51
35 36 0.318120 GTTTGATTGGCCACACCCAG 59.682 55.000 3.88 0.00 37.83 4.45
36 37 0.187117 TTTGATTGGCCACACCCAGA 59.813 50.000 3.88 0.00 37.83 3.86
37 38 0.539438 TTGATTGGCCACACCCAGAC 60.539 55.000 3.88 0.00 37.83 3.51
38 39 1.678970 GATTGGCCACACCCAGACC 60.679 63.158 3.88 0.00 37.83 3.85
39 40 2.424842 GATTGGCCACACCCAGACCA 62.425 60.000 3.88 0.00 37.83 4.02
40 41 2.713531 ATTGGCCACACCCAGACCAC 62.714 60.000 3.88 0.00 37.83 4.16
43 44 3.238497 CCACACCCAGACCACGGA 61.238 66.667 0.00 0.00 0.00 4.69
44 45 2.030562 CACACCCAGACCACGGAC 59.969 66.667 0.00 0.00 0.00 4.79
45 46 2.445085 ACACCCAGACCACGGACA 60.445 61.111 0.00 0.00 0.00 4.02
46 47 2.067605 ACACCCAGACCACGGACAA 61.068 57.895 0.00 0.00 0.00 3.18
47 48 1.147376 CACCCAGACCACGGACAAA 59.853 57.895 0.00 0.00 0.00 2.83
48 49 0.250727 CACCCAGACCACGGACAAAT 60.251 55.000 0.00 0.00 0.00 2.32
49 50 1.002659 CACCCAGACCACGGACAAATA 59.997 52.381 0.00 0.00 0.00 1.40
50 51 1.002773 ACCCAGACCACGGACAAATAC 59.997 52.381 0.00 0.00 0.00 1.89
51 52 1.278127 CCCAGACCACGGACAAATACT 59.722 52.381 0.00 0.00 0.00 2.12
52 53 2.618053 CCAGACCACGGACAAATACTC 58.382 52.381 0.00 0.00 0.00 2.59
53 54 2.618053 CAGACCACGGACAAATACTCC 58.382 52.381 0.00 0.00 0.00 3.85
54 55 1.553704 AGACCACGGACAAATACTCCC 59.446 52.381 0.00 0.00 0.00 4.30
55 56 1.553704 GACCACGGACAAATACTCCCT 59.446 52.381 0.00 0.00 0.00 4.20
56 57 2.762327 GACCACGGACAAATACTCCCTA 59.238 50.000 0.00 0.00 0.00 3.53
57 58 2.764572 ACCACGGACAAATACTCCCTAG 59.235 50.000 0.00 0.00 0.00 3.02
58 59 3.028850 CCACGGACAAATACTCCCTAGA 58.971 50.000 0.00 0.00 0.00 2.43
59 60 3.449737 CCACGGACAAATACTCCCTAGAA 59.550 47.826 0.00 0.00 0.00 2.10
60 61 4.441634 CCACGGACAAATACTCCCTAGAAG 60.442 50.000 0.00 0.00 0.00 2.85
78 79 5.743636 AGAAGAGAAGAGAAGCATCAAGT 57.256 39.130 0.00 0.00 0.00 3.16
81 84 7.096551 AGAAGAGAAGAGAAGCATCAAGTTAC 58.903 38.462 0.00 0.00 0.00 2.50
325 344 7.954788 GGTTGCATACAAAACCAATTAAAGA 57.045 32.000 0.00 0.00 44.41 2.52
326 345 8.371770 GGTTGCATACAAAACCAATTAAAGAA 57.628 30.769 0.00 0.00 44.41 2.52
327 346 8.279800 GGTTGCATACAAAACCAATTAAAGAAC 58.720 33.333 0.00 0.00 44.41 3.01
369 388 5.168569 TCTGTGTCGCCATTAAAGAACTAG 58.831 41.667 0.00 0.00 0.00 2.57
465 521 3.608474 GCAACATTTGACCCGTTCTGTAC 60.608 47.826 0.00 0.00 0.00 2.90
469 525 0.034337 TTGACCCGTTCTGTACTGCC 59.966 55.000 0.00 0.00 0.00 4.85
473 529 1.218316 CCGTTCTGTACTGCCCTCC 59.782 63.158 0.00 0.00 0.00 4.30
529 587 1.011333 CGCCCAATAACGACCGAATT 58.989 50.000 0.00 0.00 0.00 2.17
547 605 4.984785 CGAATTTGTCTGTCTCAACTCTGA 59.015 41.667 0.00 0.00 0.00 3.27
576 641 1.858399 GCACTTTCGTGGAAACCAACG 60.858 52.381 0.00 0.00 41.51 4.10
578 643 0.317519 CTTTCGTGGAAACCAACGCC 60.318 55.000 0.00 0.00 34.18 5.68
579 644 1.030488 TTTCGTGGAAACCAACGCCA 61.030 50.000 0.00 0.00 34.18 5.69
580 645 1.030488 TTCGTGGAAACCAACGCCAA 61.030 50.000 0.00 0.00 34.18 4.52
581 646 1.298788 CGTGGAAACCAACGCCAAC 60.299 57.895 0.00 0.00 34.18 3.77
582 647 1.810532 GTGGAAACCAACGCCAACA 59.189 52.632 0.00 0.00 34.18 3.33
583 648 0.387565 GTGGAAACCAACGCCAACAT 59.612 50.000 0.00 0.00 34.18 2.71
584 649 1.115467 TGGAAACCAACGCCAACATT 58.885 45.000 0.00 0.00 0.00 2.71
585 650 1.202463 TGGAAACCAACGCCAACATTG 60.202 47.619 0.00 0.00 0.00 2.82
591 656 1.472082 CCAACGCCAACATTGAGCATA 59.528 47.619 0.00 0.00 0.00 3.14
594 659 1.093972 CGCCAACATTGAGCATACCA 58.906 50.000 0.00 0.00 0.00 3.25
598 663 2.746904 CCAACATTGAGCATACCACGAA 59.253 45.455 0.00 0.00 0.00 3.85
645 4314 4.985538 TGGAGTGCCAAAAAGATTACTCT 58.014 39.130 0.00 0.00 42.49 3.24
646 4315 6.121776 TGGAGTGCCAAAAAGATTACTCTA 57.878 37.500 0.00 0.00 42.49 2.43
647 4316 5.938125 TGGAGTGCCAAAAAGATTACTCTAC 59.062 40.000 0.00 0.00 42.49 2.59
681 4350 0.454600 CCATGCATGCTTGTCACTCC 59.545 55.000 26.41 0.00 0.00 3.85
710 4379 1.468985 ACGAGAGTGATCTGGACTGG 58.531 55.000 0.00 0.00 46.97 4.00
711 4380 1.004862 ACGAGAGTGATCTGGACTGGA 59.995 52.381 0.00 0.00 46.97 3.86
712 4381 1.675483 CGAGAGTGATCTGGACTGGAG 59.325 57.143 0.00 0.00 0.00 3.86
713 4382 2.031120 GAGAGTGATCTGGACTGGAGG 58.969 57.143 0.00 0.00 0.00 4.30
715 4384 0.980231 AGTGATCTGGACTGGAGGCC 60.980 60.000 0.00 0.00 0.00 5.19
716 4385 1.080907 TGATCTGGACTGGAGGCCA 59.919 57.895 5.01 0.05 0.00 5.36
717 4386 0.326904 TGATCTGGACTGGAGGCCAT 60.327 55.000 5.01 0.00 32.89 4.40
718 4387 0.396060 GATCTGGACTGGAGGCCATC 59.604 60.000 5.01 0.00 32.89 3.51
719 4388 1.406065 ATCTGGACTGGAGGCCATCG 61.406 60.000 5.01 0.00 32.89 3.84
721 4390 2.303549 CTGGACTGGAGGCCATCGTC 62.304 65.000 5.01 5.70 32.89 4.20
722 4391 2.060980 GGACTGGAGGCCATCGTCT 61.061 63.158 5.01 0.00 31.83 4.18
723 4392 1.142748 GACTGGAGGCCATCGTCTG 59.857 63.158 5.01 0.00 30.82 3.51
724 4393 2.202987 CTGGAGGCCATCGTCTGC 60.203 66.667 5.01 0.00 30.82 4.26
725 4394 4.147449 TGGAGGCCATCGTCTGCG 62.147 66.667 5.01 0.00 39.92 5.18
766 5514 4.504916 CTCCGTCGCCTCAGCCAG 62.505 72.222 0.00 0.00 34.57 4.85
864 5612 2.554032 CCCAGAGCCGCCATTTTTATAG 59.446 50.000 0.00 0.00 0.00 1.31
960 5716 1.065102 GCTCCATACTCGTCGCACTTA 59.935 52.381 0.00 0.00 0.00 2.24
965 5721 1.162698 TACTCGTCGCACTTAGCACT 58.837 50.000 0.00 0.00 46.13 4.40
966 5722 0.314302 ACTCGTCGCACTTAGCACTT 59.686 50.000 0.00 0.00 46.13 3.16
967 5723 1.538512 ACTCGTCGCACTTAGCACTTA 59.461 47.619 0.00 0.00 46.13 2.24
968 5724 2.177977 CTCGTCGCACTTAGCACTTAG 58.822 52.381 0.00 0.00 46.13 2.18
1116 6246 0.400975 GCATGCTCATGGAGGAGGAT 59.599 55.000 11.37 0.00 45.43 3.24
1425 6600 1.664649 CTCGTTCCTTGCTGACGCA 60.665 57.895 0.00 0.00 46.24 5.24
1702 6882 0.609406 GGAGGAGGCCAACAAGTTCC 60.609 60.000 5.01 0.00 0.00 3.62
2001 7199 0.108585 ACAGCGAGGCCAAGAAGAAA 59.891 50.000 5.01 0.00 0.00 2.52
2070 7268 1.818363 CATGCTCATCCACTGCGCT 60.818 57.895 9.73 0.00 36.52 5.92
2295 7493 3.434319 AAGCTGTTCATGGCGGCG 61.434 61.111 0.51 0.51 42.62 6.46
2353 7551 2.264480 CCATCCTGAACGCCGTGA 59.736 61.111 0.00 0.00 0.00 4.35
3291 8599 4.162509 GCAACAAGAATACTACTCCCTCCT 59.837 45.833 0.00 0.00 0.00 3.69
3295 8603 6.023603 ACAAGAATACTACTCCCTCCTTTCA 58.976 40.000 0.00 0.00 0.00 2.69
3296 8604 6.674419 ACAAGAATACTACTCCCTCCTTTCAT 59.326 38.462 0.00 0.00 0.00 2.57
3297 8605 7.182930 ACAAGAATACTACTCCCTCCTTTCATT 59.817 37.037 0.00 0.00 0.00 2.57
3298 8606 7.757242 AGAATACTACTCCCTCCTTTCATTT 57.243 36.000 0.00 0.00 0.00 2.32
3306 8614 7.575499 ACTCCCTCCTTTCATTTATATAGGG 57.425 40.000 0.00 0.00 43.23 3.53
3308 8616 5.253096 TCCCTCCTTTCATTTATATAGGGCC 59.747 44.000 0.00 0.00 41.88 5.80
3309 8617 5.015178 CCCTCCTTTCATTTATATAGGGCCA 59.985 44.000 6.18 0.00 36.30 5.36
3312 8620 7.675619 CCTCCTTTCATTTATATAGGGCCAAAT 59.324 37.037 6.18 0.69 0.00 2.32
3313 8621 8.421249 TCCTTTCATTTATATAGGGCCAAATG 57.579 34.615 16.25 16.25 38.92 2.32
3314 8622 7.039082 TCCTTTCATTTATATAGGGCCAAATGC 60.039 37.037 17.14 0.00 37.96 3.56
3315 8623 5.895636 TCATTTATATAGGGCCAAATGCG 57.104 39.130 17.14 1.04 42.61 4.73
3316 8624 5.321102 TCATTTATATAGGGCCAAATGCGT 58.679 37.500 17.14 0.00 42.61 5.24
3318 8626 6.266558 TCATTTATATAGGGCCAAATGCGTTT 59.733 34.615 17.14 0.00 42.61 3.60
3320 8628 6.472686 TTATATAGGGCCAAATGCGTTTTT 57.527 33.333 6.18 0.00 42.61 1.94
3321 8629 2.734276 TAGGGCCAAATGCGTTTTTC 57.266 45.000 6.18 0.00 42.61 2.29
3325 8633 2.356069 GGGCCAAATGCGTTTTTCAAAA 59.644 40.909 4.39 0.00 42.61 2.44
3326 8634 3.358775 GGCCAAATGCGTTTTTCAAAAC 58.641 40.909 0.00 5.25 43.61 2.43
3327 8635 3.358775 GCCAAATGCGTTTTTCAAAACC 58.641 40.909 0.00 3.93 44.05 3.27
3328 8636 3.181506 GCCAAATGCGTTTTTCAAAACCA 60.182 39.130 0.00 8.53 44.05 3.67
3329 8637 4.672801 GCCAAATGCGTTTTTCAAAACCAA 60.673 37.500 0.00 0.00 44.05 3.67
3330 8638 4.790651 CCAAATGCGTTTTTCAAAACCAAC 59.209 37.500 0.00 1.44 44.05 3.77
3332 8640 5.871465 AATGCGTTTTTCAAAACCAACTT 57.129 30.435 9.12 0.50 44.05 2.66
3336 8644 5.076765 GCGTTTTTCAAAACCAACTTTGAC 58.923 37.500 9.12 0.00 43.29 3.18
3339 8647 7.201487 GCGTTTTTCAAAACCAACTTTGACTAT 60.201 33.333 9.12 0.00 43.29 2.12
3340 8648 8.652463 CGTTTTTCAAAACCAACTTTGACTATT 58.348 29.630 9.12 0.00 43.29 1.73
3341 8649 9.753669 GTTTTTCAAAACCAACTTTGACTATTG 57.246 29.630 4.09 0.00 43.29 1.90
3343 8651 8.696410 TTTCAAAACCAACTTTGACTATTGAC 57.304 30.769 0.00 0.00 43.29 3.18
3346 8654 7.973388 TCAAAACCAACTTTGACTATTGACAAG 59.027 33.333 0.00 0.00 39.74 3.16
3348 8656 7.823745 AACCAACTTTGACTATTGACAAGAT 57.176 32.000 0.00 0.00 0.00 2.40
3350 8658 8.918202 ACCAACTTTGACTATTGACAAGATTA 57.082 30.769 0.00 0.00 0.00 1.75
3351 8659 9.349713 ACCAACTTTGACTATTGACAAGATTAA 57.650 29.630 0.00 0.00 0.00 1.40
3417 8725 9.657419 AAAATCCTTTCACATATGAATTTGACC 57.343 29.630 10.38 0.00 44.36 4.02
3418 8726 6.435430 TCCTTTCACATATGAATTTGACCG 57.565 37.500 10.38 0.00 44.36 4.79
3419 8727 5.943416 TCCTTTCACATATGAATTTGACCGT 59.057 36.000 10.38 0.00 44.36 4.83
3420 8728 7.106890 TCCTTTCACATATGAATTTGACCGTA 58.893 34.615 10.38 0.00 44.36 4.02
3421 8729 7.773224 TCCTTTCACATATGAATTTGACCGTAT 59.227 33.333 10.38 0.00 44.36 3.06
3422 8730 9.051679 CCTTTCACATATGAATTTGACCGTATA 57.948 33.333 10.38 0.00 44.36 1.47
3423 8731 9.864034 CTTTCACATATGAATTTGACCGTATAC 57.136 33.333 10.38 0.00 44.36 1.47
3424 8732 9.607988 TTTCACATATGAATTTGACCGTATACT 57.392 29.630 10.38 0.00 44.36 2.12
3425 8733 9.607988 TTCACATATGAATTTGACCGTATACTT 57.392 29.630 10.38 0.00 40.01 2.24
3426 8734 9.256477 TCACATATGAATTTGACCGTATACTTC 57.744 33.333 10.38 0.00 0.00 3.01
3427 8735 8.214472 CACATATGAATTTGACCGTATACTTCG 58.786 37.037 10.38 0.00 0.00 3.79
3428 8736 7.924412 ACATATGAATTTGACCGTATACTTCGT 59.076 33.333 10.38 0.74 0.00 3.85
3429 8737 6.583912 ATGAATTTGACCGTATACTTCGTG 57.416 37.500 0.56 0.00 0.00 4.35
3430 8738 5.472148 TGAATTTGACCGTATACTTCGTGT 58.528 37.500 0.56 0.00 0.00 4.49
3431 8739 6.619744 TGAATTTGACCGTATACTTCGTGTA 58.380 36.000 0.56 0.00 35.37 2.90
3432 8740 7.089538 TGAATTTGACCGTATACTTCGTGTAA 58.910 34.615 0.56 0.00 34.45 2.41
3433 8741 7.274033 TGAATTTGACCGTATACTTCGTGTAAG 59.726 37.037 0.56 0.00 41.33 2.34
3435 8743 5.627499 TGACCGTATACTTCGTGTAAGTT 57.373 39.130 0.56 0.00 46.61 2.66
3436 8744 5.393124 TGACCGTATACTTCGTGTAAGTTG 58.607 41.667 0.56 0.00 46.61 3.16
3437 8745 4.168760 ACCGTATACTTCGTGTAAGTTGC 58.831 43.478 0.56 0.00 46.61 4.17
3438 8746 4.168014 CCGTATACTTCGTGTAAGTTGCA 58.832 43.478 0.56 0.00 46.61 4.08
3439 8747 4.802039 CCGTATACTTCGTGTAAGTTGCAT 59.198 41.667 0.56 0.00 46.61 3.96
3440 8748 5.276207 CCGTATACTTCGTGTAAGTTGCATG 60.276 44.000 6.82 6.82 46.61 4.06
3441 8749 5.287752 CGTATACTTCGTGTAAGTTGCATGT 59.712 40.000 12.19 5.43 46.61 3.21
3442 8750 5.779806 ATACTTCGTGTAAGTTGCATGTC 57.220 39.130 12.19 0.00 46.61 3.06
3443 8751 3.462982 ACTTCGTGTAAGTTGCATGTCA 58.537 40.909 12.19 1.50 46.61 3.58
3444 8752 4.065088 ACTTCGTGTAAGTTGCATGTCAT 58.935 39.130 12.19 0.00 46.61 3.06
3445 8753 5.234752 ACTTCGTGTAAGTTGCATGTCATA 58.765 37.500 12.19 0.00 46.61 2.15
3446 8754 5.874810 ACTTCGTGTAAGTTGCATGTCATAT 59.125 36.000 12.19 0.00 46.61 1.78
3447 8755 7.039270 ACTTCGTGTAAGTTGCATGTCATATA 58.961 34.615 12.19 0.00 46.61 0.86
3448 8756 7.710907 ACTTCGTGTAAGTTGCATGTCATATAT 59.289 33.333 12.19 0.00 46.61 0.86
3449 8757 8.432110 TTCGTGTAAGTTGCATGTCATATATT 57.568 30.769 12.19 0.00 0.00 1.28
3450 8758 9.535878 TTCGTGTAAGTTGCATGTCATATATTA 57.464 29.630 12.19 0.00 0.00 0.98
3451 8759 9.705290 TCGTGTAAGTTGCATGTCATATATTAT 57.295 29.630 12.19 0.00 0.00 1.28
3477 8785 7.203255 ACTCTAACATTTGGTCAAAGTTAGC 57.797 36.000 22.83 0.00 39.10 3.09
3478 8786 6.206829 ACTCTAACATTTGGTCAAAGTTAGCC 59.793 38.462 22.83 0.00 39.10 3.93
3479 8787 6.303839 TCTAACATTTGGTCAAAGTTAGCCT 58.696 36.000 22.83 1.72 39.10 4.58
3480 8788 5.453567 AACATTTGGTCAAAGTTAGCCTC 57.546 39.130 2.55 0.00 33.32 4.70
3481 8789 3.502211 ACATTTGGTCAAAGTTAGCCTCG 59.498 43.478 2.55 0.00 33.32 4.63
3482 8790 3.478857 TTTGGTCAAAGTTAGCCTCGA 57.521 42.857 0.00 0.00 0.00 4.04
3483 8791 3.478857 TTGGTCAAAGTTAGCCTCGAA 57.521 42.857 0.00 0.00 0.00 3.71
3484 8792 3.478857 TGGTCAAAGTTAGCCTCGAAA 57.521 42.857 0.00 0.00 0.00 3.46
3485 8793 3.811083 TGGTCAAAGTTAGCCTCGAAAA 58.189 40.909 0.00 0.00 0.00 2.29
3486 8794 4.394729 TGGTCAAAGTTAGCCTCGAAAAT 58.605 39.130 0.00 0.00 0.00 1.82
3487 8795 4.454504 TGGTCAAAGTTAGCCTCGAAAATC 59.545 41.667 0.00 0.00 0.00 2.17
3488 8796 4.435651 GGTCAAAGTTAGCCTCGAAAATCG 60.436 45.833 0.00 0.00 42.10 3.34
3489 8797 3.124636 TCAAAGTTAGCCTCGAAAATCGC 59.875 43.478 0.00 0.00 40.21 4.58
3490 8798 2.380084 AGTTAGCCTCGAAAATCGCA 57.620 45.000 0.00 0.00 40.21 5.10
3491 8799 2.906354 AGTTAGCCTCGAAAATCGCAT 58.094 42.857 0.00 0.00 40.21 4.73
3492 8800 3.270877 AGTTAGCCTCGAAAATCGCATT 58.729 40.909 0.00 0.00 40.21 3.56
3493 8801 4.439057 AGTTAGCCTCGAAAATCGCATTA 58.561 39.130 0.00 0.00 40.21 1.90
3494 8802 4.508124 AGTTAGCCTCGAAAATCGCATTAG 59.492 41.667 0.00 0.00 40.21 1.73
3495 8803 3.179443 AGCCTCGAAAATCGCATTAGA 57.821 42.857 0.00 0.00 40.21 2.10
3496 8804 2.866762 AGCCTCGAAAATCGCATTAGAC 59.133 45.455 0.00 0.00 40.21 2.59
3501 8809 2.605818 CGAAAATCGCATTAGACCGGAA 59.394 45.455 9.46 0.00 31.14 4.30
3518 8826 4.957684 CGGAAGGAGGGAGTATGTAAAT 57.042 45.455 0.00 0.00 0.00 1.40
3741 10148 3.207669 GCAGCTGGGCGGATCTTG 61.208 66.667 17.12 0.00 0.00 3.02
3742 10149 2.515523 CAGCTGGGCGGATCTTGG 60.516 66.667 5.57 0.00 0.00 3.61
3743 10150 3.011517 AGCTGGGCGGATCTTGGT 61.012 61.111 0.00 0.00 0.00 3.67
3745 10152 2.115291 GCTGGGCGGATCTTGGTTC 61.115 63.158 0.00 0.00 0.00 3.62
3763 10170 3.384348 GGTCTTCCGGCCACACTA 58.616 61.111 2.24 0.00 0.00 2.74
3766 10173 1.987855 TCTTCCGGCCACACTAGGG 60.988 63.158 2.24 0.00 0.00 3.53
3815 10222 0.901827 TTTAGTCAGCTGCGGGATCA 59.098 50.000 9.47 0.00 0.00 2.92
3822 10229 2.503061 CTGCGGGATCAGAGTGGG 59.497 66.667 0.00 0.00 36.19 4.61
3844 10251 1.573829 GACTGCCGGTGAAAATCGCA 61.574 55.000 1.90 0.00 0.00 5.10
3863 10270 0.762418 ACCGACTTTGGTCATGGTGA 59.238 50.000 0.00 0.00 37.91 4.02
3875 10282 3.620419 ATGGTGAACGATGGCGGCA 62.620 57.895 16.34 16.34 43.17 5.69
3881 10288 0.451783 GAACGATGGCGGCATCTTTT 59.548 50.000 38.64 31.98 43.17 2.27
3899 10306 6.012658 TCTTTTGCATCATTGTTGTAGTCC 57.987 37.500 0.00 0.00 0.00 3.85
3909 10316 2.313317 TGTTGTAGTCCGTCTCACCTT 58.687 47.619 0.00 0.00 0.00 3.50
3920 10327 4.704833 TCACCTTGCTCGGGCTGC 62.705 66.667 9.62 0.00 39.59 5.25
3922 10329 3.003173 ACCTTGCTCGGGCTGCTA 61.003 61.111 9.62 0.00 39.59 3.49
3954 10363 3.643792 CCTAGATTTGGGTCTCTCGGATT 59.356 47.826 0.00 0.00 0.00 3.01
3958 10367 1.651737 TTGGGTCTCTCGGATTGGAA 58.348 50.000 0.00 0.00 0.00 3.53
3970 10379 0.931005 GATTGGAAGATGACGACGCC 59.069 55.000 0.00 0.00 0.00 5.68
3989 10398 2.230660 CCTTTGGTGTTGTTCTCCCTC 58.769 52.381 0.00 0.00 0.00 4.30
3990 10399 2.422803 CCTTTGGTGTTGTTCTCCCTCA 60.423 50.000 0.00 0.00 0.00 3.86
3993 10402 0.472471 GGTGTTGTTCTCCCTCACCA 59.528 55.000 7.61 0.00 45.22 4.17
4005 10414 0.804989 CCTCACCAAGGCATCGTTTC 59.195 55.000 0.00 0.00 38.67 2.78
4066 10475 4.384846 GGTGTTATATCTACCGCATCAACG 59.615 45.833 0.00 0.00 0.00 4.10
4103 10512 0.388520 CGTGGCACAACGAGATCTCA 60.389 55.000 22.31 0.00 44.16 3.27
4139 10549 1.298859 GGATGGTTGTGTGTCTCGCC 61.299 60.000 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.199097 CAAACGGTGCCATGACCTTAC 59.801 52.381 0.00 0.00 33.35 2.34
1 2 1.072489 TCAAACGGTGCCATGACCTTA 59.928 47.619 0.00 0.00 33.35 2.69
2 3 0.179004 TCAAACGGTGCCATGACCTT 60.179 50.000 0.00 0.00 33.35 3.50
3 4 0.038166 ATCAAACGGTGCCATGACCT 59.962 50.000 0.00 0.00 33.35 3.85
4 5 0.887933 AATCAAACGGTGCCATGACC 59.112 50.000 0.00 0.00 0.00 4.02
5 6 1.402720 CCAATCAAACGGTGCCATGAC 60.403 52.381 0.00 0.00 0.00 3.06
6 7 0.887247 CCAATCAAACGGTGCCATGA 59.113 50.000 0.00 0.00 0.00 3.07
7 8 0.737019 GCCAATCAAACGGTGCCATG 60.737 55.000 0.00 0.00 0.00 3.66
8 9 1.591183 GCCAATCAAACGGTGCCAT 59.409 52.632 0.00 0.00 0.00 4.40
9 10 2.569354 GGCCAATCAAACGGTGCCA 61.569 57.895 0.00 0.00 38.73 4.92
10 11 2.261361 GGCCAATCAAACGGTGCC 59.739 61.111 0.00 0.00 0.00 5.01
11 12 1.372872 GTGGCCAATCAAACGGTGC 60.373 57.895 7.24 0.00 0.00 5.01
12 13 0.318614 GTGTGGCCAATCAAACGGTG 60.319 55.000 7.24 0.00 0.00 4.94
13 14 1.460273 GGTGTGGCCAATCAAACGGT 61.460 55.000 7.24 0.00 37.17 4.83
14 15 1.288752 GGTGTGGCCAATCAAACGG 59.711 57.895 7.24 0.00 37.17 4.44
15 16 1.288752 GGGTGTGGCCAATCAAACG 59.711 57.895 7.24 0.00 39.65 3.60
16 17 0.318120 CTGGGTGTGGCCAATCAAAC 59.682 55.000 7.24 0.59 39.65 2.93
17 18 0.187117 TCTGGGTGTGGCCAATCAAA 59.813 50.000 7.24 0.00 39.65 2.69
18 19 0.539438 GTCTGGGTGTGGCCAATCAA 60.539 55.000 7.24 0.00 39.65 2.57
19 20 1.074775 GTCTGGGTGTGGCCAATCA 59.925 57.895 7.24 0.00 39.65 2.57
20 21 1.678970 GGTCTGGGTGTGGCCAATC 60.679 63.158 7.24 2.89 39.65 2.67
21 22 2.440599 GGTCTGGGTGTGGCCAAT 59.559 61.111 7.24 0.00 39.65 3.16
22 23 3.099841 TGGTCTGGGTGTGGCCAA 61.100 61.111 7.24 0.00 39.65 4.52
23 24 3.884774 GTGGTCTGGGTGTGGCCA 61.885 66.667 0.00 0.00 39.65 5.36
26 27 3.238497 TCCGTGGTCTGGGTGTGG 61.238 66.667 0.00 0.00 0.00 4.17
27 28 2.030562 GTCCGTGGTCTGGGTGTG 59.969 66.667 0.00 0.00 0.00 3.82
28 29 1.628238 TTTGTCCGTGGTCTGGGTGT 61.628 55.000 0.00 0.00 0.00 4.16
29 30 0.250727 ATTTGTCCGTGGTCTGGGTG 60.251 55.000 0.00 0.00 0.00 4.61
30 31 1.002773 GTATTTGTCCGTGGTCTGGGT 59.997 52.381 0.00 0.00 0.00 4.51
31 32 1.278127 AGTATTTGTCCGTGGTCTGGG 59.722 52.381 0.00 0.00 0.00 4.45
32 33 2.618053 GAGTATTTGTCCGTGGTCTGG 58.382 52.381 0.00 0.00 0.00 3.86
33 34 2.618053 GGAGTATTTGTCCGTGGTCTG 58.382 52.381 0.00 0.00 0.00 3.51
34 35 1.553704 GGGAGTATTTGTCCGTGGTCT 59.446 52.381 0.00 0.00 34.56 3.85
35 36 1.553704 AGGGAGTATTTGTCCGTGGTC 59.446 52.381 0.00 0.00 34.56 4.02
36 37 1.652947 AGGGAGTATTTGTCCGTGGT 58.347 50.000 0.00 0.00 34.56 4.16
37 38 3.028850 TCTAGGGAGTATTTGTCCGTGG 58.971 50.000 0.00 0.00 34.56 4.94
38 39 4.401519 TCTTCTAGGGAGTATTTGTCCGTG 59.598 45.833 0.00 0.00 34.56 4.94
39 40 4.607239 TCTTCTAGGGAGTATTTGTCCGT 58.393 43.478 0.00 0.00 34.56 4.69
40 41 4.888239 TCTCTTCTAGGGAGTATTTGTCCG 59.112 45.833 11.46 0.00 34.56 4.79
41 42 6.608002 TCTTCTCTTCTAGGGAGTATTTGTCC 59.392 42.308 11.46 0.00 33.06 4.02
42 43 7.558444 TCTCTTCTCTTCTAGGGAGTATTTGTC 59.442 40.741 11.46 0.00 33.06 3.18
43 44 7.415086 TCTCTTCTCTTCTAGGGAGTATTTGT 58.585 38.462 11.46 0.00 33.06 2.83
44 45 7.889873 TCTCTTCTCTTCTAGGGAGTATTTG 57.110 40.000 11.46 3.63 33.06 2.32
45 46 7.069455 GCTTCTCTTCTCTTCTAGGGAGTATTT 59.931 40.741 11.46 0.00 33.06 1.40
46 47 6.549736 GCTTCTCTTCTCTTCTAGGGAGTATT 59.450 42.308 11.46 0.00 33.06 1.89
47 48 6.068670 GCTTCTCTTCTCTTCTAGGGAGTAT 58.931 44.000 11.46 0.00 33.06 2.12
48 49 5.044772 TGCTTCTCTTCTCTTCTAGGGAGTA 60.045 44.000 11.46 4.15 33.06 2.59
49 50 4.264172 TGCTTCTCTTCTCTTCTAGGGAGT 60.264 45.833 11.46 0.00 33.06 3.85
50 51 4.277476 TGCTTCTCTTCTCTTCTAGGGAG 58.723 47.826 7.14 7.14 0.00 4.30
51 52 4.323569 TGCTTCTCTTCTCTTCTAGGGA 57.676 45.455 0.00 0.00 0.00 4.20
52 53 4.648762 TGATGCTTCTCTTCTCTTCTAGGG 59.351 45.833 0.88 0.00 0.00 3.53
53 54 5.850557 TGATGCTTCTCTTCTCTTCTAGG 57.149 43.478 0.88 0.00 0.00 3.02
54 55 6.866480 ACTTGATGCTTCTCTTCTCTTCTAG 58.134 40.000 0.88 0.00 0.00 2.43
55 56 6.849085 ACTTGATGCTTCTCTTCTCTTCTA 57.151 37.500 0.88 0.00 0.00 2.10
56 57 5.743636 ACTTGATGCTTCTCTTCTCTTCT 57.256 39.130 0.88 0.00 0.00 2.85
57 58 6.870965 TGTAACTTGATGCTTCTCTTCTCTTC 59.129 38.462 0.88 0.00 0.00 2.87
58 59 6.763355 TGTAACTTGATGCTTCTCTTCTCTT 58.237 36.000 0.88 0.00 0.00 2.85
59 60 6.210385 TCTGTAACTTGATGCTTCTCTTCTCT 59.790 38.462 0.88 0.00 0.00 3.10
60 61 6.393990 TCTGTAACTTGATGCTTCTCTTCTC 58.606 40.000 0.88 0.00 0.00 2.87
78 79 2.364324 ACGTGCTTGACCTCTTCTGTAA 59.636 45.455 0.00 0.00 0.00 2.41
81 84 1.143305 CACGTGCTTGACCTCTTCTG 58.857 55.000 0.82 0.00 0.00 3.02
318 337 5.552178 AGTTCTGCGAGGAAGTTCTTTAAT 58.448 37.500 2.25 0.00 0.00 1.40
319 338 4.957296 AGTTCTGCGAGGAAGTTCTTTAA 58.043 39.130 2.25 0.00 0.00 1.52
323 342 3.477210 AAAGTTCTGCGAGGAAGTTCT 57.523 42.857 2.25 0.00 37.73 3.01
325 344 3.809905 AGAAAAGTTCTGCGAGGAAGTT 58.190 40.909 5.45 5.45 38.91 2.66
326 345 3.070302 AGAGAAAAGTTCTGCGAGGAAGT 59.930 43.478 0.00 0.00 40.87 3.01
327 346 3.431572 CAGAGAAAAGTTCTGCGAGGAAG 59.568 47.826 0.00 0.00 40.87 3.46
369 388 3.558829 TCGTAGACTCGGATGTGATGTAC 59.441 47.826 0.00 0.00 0.00 2.90
451 507 1.669440 GGCAGTACAGAACGGGTCA 59.331 57.895 0.00 0.00 0.00 4.02
469 525 0.031994 CCAAACCACAAAAGCGGAGG 59.968 55.000 0.00 0.00 0.00 4.30
473 529 0.593773 CCGACCAAACCACAAAAGCG 60.594 55.000 0.00 0.00 0.00 4.68
509 567 0.108041 ATTCGGTCGTTATTGGGCGT 60.108 50.000 0.00 0.00 0.00 5.68
529 587 3.386078 AGCTTCAGAGTTGAGACAGACAA 59.614 43.478 0.00 0.00 34.15 3.18
547 605 3.386543 ACGAAAGTGCAGTGAGCTT 57.613 47.368 0.00 0.00 46.97 3.74
576 641 1.202177 CGTGGTATGCTCAATGTTGGC 60.202 52.381 0.00 0.00 0.00 4.52
578 643 4.621068 ATTCGTGGTATGCTCAATGTTG 57.379 40.909 0.00 0.00 0.00 3.33
579 644 5.296780 CCTAATTCGTGGTATGCTCAATGTT 59.703 40.000 0.00 0.00 0.00 2.71
580 645 4.816385 CCTAATTCGTGGTATGCTCAATGT 59.184 41.667 0.00 0.00 0.00 2.71
581 646 4.816385 ACCTAATTCGTGGTATGCTCAATG 59.184 41.667 0.00 0.00 34.36 2.82
582 647 5.036117 ACCTAATTCGTGGTATGCTCAAT 57.964 39.130 0.00 0.00 34.36 2.57
583 648 4.481368 ACCTAATTCGTGGTATGCTCAA 57.519 40.909 0.00 0.00 34.36 3.02
584 649 4.439057 GAACCTAATTCGTGGTATGCTCA 58.561 43.478 0.00 0.00 35.17 4.26
585 650 3.808174 GGAACCTAATTCGTGGTATGCTC 59.192 47.826 0.00 0.00 38.31 4.26
594 659 8.314751 CAATATCTATCCAGGAACCTAATTCGT 58.685 37.037 0.00 0.00 38.31 3.85
598 663 7.574021 TGCAATATCTATCCAGGAACCTAAT 57.426 36.000 0.00 0.00 0.00 1.73
656 4325 1.814394 GACAAGCATGCATGGTGAGAA 59.186 47.619 30.51 0.00 38.70 2.87
681 4350 0.673956 TCACTCTCGTCTCTCCCACG 60.674 60.000 0.00 0.00 38.67 4.94
706 4375 3.023949 GCAGACGATGGCCTCCAGT 62.024 63.158 3.32 0.00 36.75 4.00
707 4376 2.202987 GCAGACGATGGCCTCCAG 60.203 66.667 3.32 0.00 36.75 3.86
708 4377 4.147449 CGCAGACGATGGCCTCCA 62.147 66.667 3.32 0.00 43.93 3.86
725 4394 3.330853 GACGACATGCGATCCGGC 61.331 66.667 14.88 0.07 44.57 6.13
727 4396 1.658717 GGAGACGACATGCGATCCG 60.659 63.158 14.88 4.01 44.57 4.18
728 4397 0.318275 GAGGAGACGACATGCGATCC 60.318 60.000 19.73 19.73 44.27 3.36
729 4398 0.318275 GGAGGAGACGACATGCGATC 60.318 60.000 14.88 11.62 44.57 3.69
763 5511 0.461548 TAGAATGCGACTCTGGCTGG 59.538 55.000 0.00 0.00 0.00 4.85
764 5512 1.135915 ACTAGAATGCGACTCTGGCTG 59.864 52.381 0.00 0.00 0.00 4.85
765 5513 1.407258 GACTAGAATGCGACTCTGGCT 59.593 52.381 0.00 0.00 0.00 4.75
766 5514 1.407258 AGACTAGAATGCGACTCTGGC 59.593 52.381 0.00 0.00 0.00 4.85
960 5716 2.125912 CGAGGCGTGCTAAGTGCT 60.126 61.111 0.00 0.00 43.37 4.40
965 5721 1.141019 CTTAGGCGAGGCGTGCTAA 59.859 57.895 4.10 0.00 0.00 3.09
966 5722 2.805546 CTTAGGCGAGGCGTGCTA 59.194 61.111 4.10 0.00 0.00 3.49
967 5723 4.821589 GCTTAGGCGAGGCGTGCT 62.822 66.667 4.10 0.00 0.00 4.40
972 5728 2.107953 CTCTGGCTTAGGCGAGGC 59.892 66.667 8.96 9.87 43.11 4.70
973 5729 1.617947 AACCTCTGGCTTAGGCGAGG 61.618 60.000 29.38 29.38 45.85 4.63
975 5731 1.596934 CAACCTCTGGCTTAGGCGA 59.403 57.895 0.40 1.00 37.67 5.54
976 5732 2.109126 GCAACCTCTGGCTTAGGCG 61.109 63.158 0.40 0.00 37.67 5.52
977 5733 3.911137 GCAACCTCTGGCTTAGGC 58.089 61.111 0.00 0.00 37.67 3.93
1116 6246 4.696877 TGGTAGAAGAACTTGTCGTCGATA 59.303 41.667 0.00 0.00 39.50 2.92
1456 6631 4.193334 GGCCGCGCCCTTGAATTC 62.193 66.667 0.00 0.00 44.06 2.17
1533 6708 2.478033 CGCCGGGCCATTTAAGACC 61.478 63.158 14.55 0.00 0.00 3.85
1702 6882 2.551912 GGGTGTTGTTGGTCGGCAG 61.552 63.158 0.00 0.00 0.00 4.85
1758 6944 0.037232 CCACCTCGTCCTTCTTCACC 60.037 60.000 0.00 0.00 0.00 4.02
1761 6947 1.446272 CGCCACCTCGTCCTTCTTC 60.446 63.158 0.00 0.00 0.00 2.87
1768 6954 2.511600 CCCATTCGCCACCTCGTC 60.512 66.667 0.00 0.00 0.00 4.20
1769 6955 3.000819 TCCCATTCGCCACCTCGT 61.001 61.111 0.00 0.00 0.00 4.18
1770 6956 2.511600 GTCCCATTCGCCACCTCG 60.512 66.667 0.00 0.00 0.00 4.63
2021 7219 0.108567 GACCGCCTCACTCTTCTTCC 60.109 60.000 0.00 0.00 0.00 3.46
2295 7493 1.174712 TGGCCTTCTTGAAGCAGCAC 61.175 55.000 3.32 0.00 0.00 4.40
2634 7832 4.357947 TGCACGACGAGCACCTCC 62.358 66.667 16.10 0.00 37.02 4.30
3213 8421 8.547481 TGAACCATAGATCTCTGTTGGTAATA 57.453 34.615 15.81 6.77 40.58 0.98
3214 8422 7.126421 ACTGAACCATAGATCTCTGTTGGTAAT 59.874 37.037 15.81 5.81 40.58 1.89
3218 8426 5.114780 CACTGAACCATAGATCTCTGTTGG 58.885 45.833 0.00 5.46 36.92 3.77
3291 8599 6.266558 ACGCATTTGGCCCTATATAAATGAAA 59.733 34.615 21.82 3.98 40.94 2.69
3295 8603 6.664428 AAACGCATTTGGCCCTATATAAAT 57.336 33.333 0.00 0.00 40.31 1.40
3296 8604 6.472686 AAAACGCATTTGGCCCTATATAAA 57.527 33.333 0.00 0.00 40.31 1.40
3297 8605 6.096987 TGAAAAACGCATTTGGCCCTATATAA 59.903 34.615 0.00 0.00 40.31 0.98
3298 8606 5.594725 TGAAAAACGCATTTGGCCCTATATA 59.405 36.000 0.00 0.00 40.31 0.86
3302 8610 1.964223 TGAAAAACGCATTTGGCCCTA 59.036 42.857 0.00 0.00 40.31 3.53
3304 8612 1.587547 TTGAAAAACGCATTTGGCCC 58.412 45.000 0.00 0.00 40.31 5.80
3306 8614 3.181506 TGGTTTTGAAAAACGCATTTGGC 60.182 39.130 11.43 0.00 47.00 4.52
3308 8616 5.626211 AGTTGGTTTTGAAAAACGCATTTG 58.374 33.333 11.43 0.00 47.00 2.32
3309 8617 5.871465 AGTTGGTTTTGAAAAACGCATTT 57.129 30.435 11.43 0.00 47.00 2.32
3312 8620 4.750098 TCAAAGTTGGTTTTGAAAAACGCA 59.250 33.333 11.43 8.48 47.00 5.24
3313 8621 5.076765 GTCAAAGTTGGTTTTGAAAAACGC 58.923 37.500 11.43 6.44 45.62 4.84
3314 8622 6.460664 AGTCAAAGTTGGTTTTGAAAAACG 57.539 33.333 11.43 0.00 45.62 3.60
3315 8623 9.753669 CAATAGTCAAAGTTGGTTTTGAAAAAC 57.246 29.630 9.66 9.66 45.62 2.43
3316 8624 9.712305 TCAATAGTCAAAGTTGGTTTTGAAAAA 57.288 25.926 3.05 0.00 45.62 1.94
3318 8626 8.307483 TGTCAATAGTCAAAGTTGGTTTTGAAA 58.693 29.630 3.05 0.00 45.62 2.69
3320 8628 7.397892 TGTCAATAGTCAAAGTTGGTTTTGA 57.602 32.000 0.00 0.00 42.93 2.69
3321 8629 7.973388 TCTTGTCAATAGTCAAAGTTGGTTTTG 59.027 33.333 0.00 0.00 38.97 2.44
3325 8633 7.823745 AATCTTGTCAATAGTCAAAGTTGGT 57.176 32.000 0.00 0.00 0.00 3.67
3391 8699 9.657419 GGTCAAATTCATATGTGAAAGGATTTT 57.343 29.630 9.08 2.38 46.67 1.82
3392 8700 7.975616 CGGTCAAATTCATATGTGAAAGGATTT 59.024 33.333 9.08 2.73 46.67 2.17
3393 8701 7.122650 ACGGTCAAATTCATATGTGAAAGGATT 59.877 33.333 9.08 0.00 46.67 3.01
3394 8702 6.603201 ACGGTCAAATTCATATGTGAAAGGAT 59.397 34.615 9.08 0.00 46.67 3.24
3395 8703 5.943416 ACGGTCAAATTCATATGTGAAAGGA 59.057 36.000 9.08 4.65 46.67 3.36
3396 8704 6.194796 ACGGTCAAATTCATATGTGAAAGG 57.805 37.500 9.08 2.43 46.67 3.11
3397 8705 9.864034 GTATACGGTCAAATTCATATGTGAAAG 57.136 33.333 9.08 3.12 46.67 2.62
3398 8706 9.607988 AGTATACGGTCAAATTCATATGTGAAA 57.392 29.630 9.08 0.00 46.67 2.69
3400 8708 9.256477 GAAGTATACGGTCAAATTCATATGTGA 57.744 33.333 1.90 0.00 0.00 3.58
3401 8709 8.214472 CGAAGTATACGGTCAAATTCATATGTG 58.786 37.037 1.90 0.00 0.00 3.21
3402 8710 7.924412 ACGAAGTATACGGTCAAATTCATATGT 59.076 33.333 1.90 0.00 41.94 2.29
3403 8711 8.214472 CACGAAGTATACGGTCAAATTCATATG 58.786 37.037 0.00 0.00 41.61 1.78
3404 8712 7.924412 ACACGAAGTATACGGTCAAATTCATAT 59.076 33.333 9.42 0.00 41.61 1.78
3405 8713 7.259882 ACACGAAGTATACGGTCAAATTCATA 58.740 34.615 9.42 0.00 41.61 2.15
3406 8714 6.103997 ACACGAAGTATACGGTCAAATTCAT 58.896 36.000 9.42 0.00 41.61 2.57
3407 8715 5.472148 ACACGAAGTATACGGTCAAATTCA 58.528 37.500 9.42 0.00 41.61 2.57
3408 8716 7.510428 TTACACGAAGTATACGGTCAAATTC 57.490 36.000 9.42 1.05 41.61 2.17
3409 8717 7.515957 CTTACACGAAGTATACGGTCAAATT 57.484 36.000 9.42 0.00 41.61 1.82
3423 8731 4.668576 ATGACATGCAACTTACACGAAG 57.331 40.909 0.00 0.00 41.37 3.79
3424 8732 8.432110 AATATATGACATGCAACTTACACGAA 57.568 30.769 0.00 0.00 0.00 3.85
3425 8733 9.705290 ATAATATATGACATGCAACTTACACGA 57.295 29.630 0.00 0.00 0.00 4.35
3451 8759 8.780249 GCTAACTTTGACCAAATGTTAGAGTAA 58.220 33.333 26.48 9.61 40.08 2.24
3452 8760 7.389607 GGCTAACTTTGACCAAATGTTAGAGTA 59.610 37.037 26.48 10.01 40.08 2.59
3453 8761 6.206829 GGCTAACTTTGACCAAATGTTAGAGT 59.793 38.462 26.48 10.06 40.08 3.24
3454 8762 6.431234 AGGCTAACTTTGACCAAATGTTAGAG 59.569 38.462 26.48 16.32 40.08 2.43
3455 8763 6.303839 AGGCTAACTTTGACCAAATGTTAGA 58.696 36.000 26.48 10.83 40.08 2.10
3456 8764 6.575162 AGGCTAACTTTGACCAAATGTTAG 57.425 37.500 22.72 22.72 40.29 2.34
3457 8765 5.180492 CGAGGCTAACTTTGACCAAATGTTA 59.820 40.000 0.00 12.42 0.00 2.41
3458 8766 4.023193 CGAGGCTAACTTTGACCAAATGTT 60.023 41.667 0.00 11.80 0.00 2.71
3459 8767 3.502211 CGAGGCTAACTTTGACCAAATGT 59.498 43.478 0.00 0.00 0.00 2.71
3460 8768 3.751175 TCGAGGCTAACTTTGACCAAATG 59.249 43.478 0.00 0.00 0.00 2.32
3461 8769 4.015872 TCGAGGCTAACTTTGACCAAAT 57.984 40.909 0.00 0.00 0.00 2.32
3462 8770 3.478857 TCGAGGCTAACTTTGACCAAA 57.521 42.857 0.00 0.00 0.00 3.28
3463 8771 3.478857 TTCGAGGCTAACTTTGACCAA 57.521 42.857 0.00 0.00 0.00 3.67
3464 8772 3.478857 TTTCGAGGCTAACTTTGACCA 57.521 42.857 0.00 0.00 0.00 4.02
3465 8773 4.435651 CGATTTTCGAGGCTAACTTTGACC 60.436 45.833 0.00 0.00 43.74 4.02
3466 8774 4.638963 CGATTTTCGAGGCTAACTTTGAC 58.361 43.478 0.00 0.00 43.74 3.18
3467 8775 3.124636 GCGATTTTCGAGGCTAACTTTGA 59.875 43.478 0.32 0.00 43.74 2.69
3468 8776 3.120338 TGCGATTTTCGAGGCTAACTTTG 60.120 43.478 0.32 0.00 43.74 2.77
3469 8777 3.071479 TGCGATTTTCGAGGCTAACTTT 58.929 40.909 0.32 0.00 43.74 2.66
3470 8778 2.695359 TGCGATTTTCGAGGCTAACTT 58.305 42.857 0.32 0.00 43.74 2.66
3471 8779 2.380084 TGCGATTTTCGAGGCTAACT 57.620 45.000 0.32 0.00 43.74 2.24
3472 8780 3.675467 AATGCGATTTTCGAGGCTAAC 57.325 42.857 0.32 0.00 43.74 2.34
3473 8781 4.506654 GTCTAATGCGATTTTCGAGGCTAA 59.493 41.667 0.32 0.00 43.74 3.09
3474 8782 4.049186 GTCTAATGCGATTTTCGAGGCTA 58.951 43.478 0.32 0.00 43.74 3.93
3475 8783 2.866762 GTCTAATGCGATTTTCGAGGCT 59.133 45.455 0.32 0.00 43.74 4.58
3476 8784 2.032808 GGTCTAATGCGATTTTCGAGGC 60.033 50.000 0.32 0.00 43.74 4.70
3477 8785 2.218759 CGGTCTAATGCGATTTTCGAGG 59.781 50.000 0.32 0.00 43.74 4.63
3478 8786 2.218759 CCGGTCTAATGCGATTTTCGAG 59.781 50.000 0.32 0.00 43.74 4.04
3479 8787 2.159212 TCCGGTCTAATGCGATTTTCGA 60.159 45.455 0.00 0.00 43.74 3.71
3480 8788 2.198406 TCCGGTCTAATGCGATTTTCG 58.802 47.619 0.00 0.00 43.89 3.46
3481 8789 3.002348 CCTTCCGGTCTAATGCGATTTTC 59.998 47.826 0.00 0.00 0.00 2.29
3482 8790 2.943033 CCTTCCGGTCTAATGCGATTTT 59.057 45.455 0.00 0.00 0.00 1.82
3483 8791 2.169769 TCCTTCCGGTCTAATGCGATTT 59.830 45.455 0.00 0.00 0.00 2.17
3484 8792 1.760613 TCCTTCCGGTCTAATGCGATT 59.239 47.619 0.00 0.00 0.00 3.34
3485 8793 1.341531 CTCCTTCCGGTCTAATGCGAT 59.658 52.381 0.00 0.00 0.00 4.58
3486 8794 0.744874 CTCCTTCCGGTCTAATGCGA 59.255 55.000 0.00 0.00 0.00 5.10
3487 8795 0.249489 CCTCCTTCCGGTCTAATGCG 60.249 60.000 0.00 0.00 0.00 4.73
3488 8796 0.106894 CCCTCCTTCCGGTCTAATGC 59.893 60.000 0.00 0.00 0.00 3.56
3489 8797 1.689273 CTCCCTCCTTCCGGTCTAATG 59.311 57.143 0.00 0.00 0.00 1.90
3490 8798 1.291335 ACTCCCTCCTTCCGGTCTAAT 59.709 52.381 0.00 0.00 0.00 1.73
3491 8799 0.708802 ACTCCCTCCTTCCGGTCTAA 59.291 55.000 0.00 0.00 0.00 2.10
3492 8800 1.600058 TACTCCCTCCTTCCGGTCTA 58.400 55.000 0.00 0.00 0.00 2.59
3493 8801 0.935194 ATACTCCCTCCTTCCGGTCT 59.065 55.000 0.00 0.00 0.00 3.85
3494 8802 1.041437 CATACTCCCTCCTTCCGGTC 58.959 60.000 0.00 0.00 0.00 4.79
3495 8803 0.338814 ACATACTCCCTCCTTCCGGT 59.661 55.000 0.00 0.00 0.00 5.28
3496 8804 2.376695 TACATACTCCCTCCTTCCGG 57.623 55.000 0.00 0.00 0.00 5.14
3501 8809 6.789959 AGCATCTAATTTACATACTCCCTCCT 59.210 38.462 0.00 0.00 0.00 3.69
3651 10057 1.512926 CTGAAGACCCAACCAAGTCG 58.487 55.000 0.00 0.00 38.08 4.18
3701 10108 3.118454 CGCCGCATCTGAAACCGT 61.118 61.111 0.00 0.00 0.00 4.83
3802 10209 1.521010 CACTCTGATCCCGCAGCTG 60.521 63.158 10.11 10.11 35.86 4.24
3815 10222 2.681778 CGGCAGTCTCCCCACTCT 60.682 66.667 0.00 0.00 0.00 3.24
3822 10229 1.087501 GATTTTCACCGGCAGTCTCC 58.912 55.000 0.00 0.00 0.00 3.71
3844 10251 0.762418 TCACCATGACCAAAGTCGGT 59.238 50.000 0.00 0.00 46.74 4.69
3875 10282 6.623549 CGGACTACAACAATGATGCAAAAGAT 60.624 38.462 0.00 0.00 0.00 2.40
3881 10288 3.000041 GACGGACTACAACAATGATGCA 59.000 45.455 0.00 0.00 0.00 3.96
3887 10294 2.897969 AGGTGAGACGGACTACAACAAT 59.102 45.455 0.00 0.00 0.00 2.71
3899 10306 2.125912 CCCGAGCAAGGTGAGACG 60.126 66.667 0.00 0.00 0.00 4.18
3909 10316 3.865383 CCCATAGCAGCCCGAGCA 61.865 66.667 0.00 0.00 43.56 4.26
3948 10357 1.202256 CGTCGTCATCTTCCAATCCGA 60.202 52.381 0.00 0.00 0.00 4.55
3954 10363 0.320374 AAAGGCGTCGTCATCTTCCA 59.680 50.000 0.00 0.00 0.00 3.53
3958 10367 0.670546 CACCAAAGGCGTCGTCATCT 60.671 55.000 0.00 0.00 0.00 2.90
3970 10379 2.618709 GTGAGGGAGAACAACACCAAAG 59.381 50.000 0.00 0.00 0.00 2.77
3979 10388 1.059584 TGCCTTGGTGAGGGAGAACA 61.060 55.000 0.00 0.00 46.40 3.18
3989 10398 1.466167 CTCAGAAACGATGCCTTGGTG 59.534 52.381 0.00 0.00 0.00 4.17
3990 10399 1.813513 CTCAGAAACGATGCCTTGGT 58.186 50.000 0.00 0.00 0.00 3.67
3993 10402 1.446907 CTGCTCAGAAACGATGCCTT 58.553 50.000 0.00 0.00 0.00 4.35
4066 10475 4.803426 CTGTCGAGACCCGCTGCC 62.803 72.222 0.34 0.00 38.37 4.85
4073 10482 4.357947 TGCCACGCTGTCGAGACC 62.358 66.667 0.34 0.00 39.41 3.85
4082 10491 1.738099 GATCTCGTTGTGCCACGCT 60.738 57.895 0.00 0.00 40.14 5.07
4120 10529 1.298859 GGCGAGACACACAACCATCC 61.299 60.000 0.00 0.00 0.00 3.51
4139 10549 3.071459 GATCTCGTTGTGCCACGCG 62.071 63.158 3.53 3.53 40.14 6.01


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

AutoCloner maintained by Alex Coulton.