Multiple sequence alignment - TraesCS4A01G195900

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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 TraesCS4A01G195900 chr4A 100.000 6548 0 0 2693 9240 478211282 478217829 0.000000e+00 12092
1 TraesCS4A01G195900 chr4A 100.000 2459 0 0 1 2459 478208590 478211048 0.000000e+00 4542
2 TraesCS4A01G195900 chr4A 96.099 564 21 1 3 565 213953170 213953733 0.000000e+00 918
3 TraesCS4A01G195900 chr4A 81.194 888 139 17 1401 2268 478191411 478192290 0.000000e+00 689
4 TraesCS4A01G195900 chr4A 94.811 212 7 3 2249 2459 667160381 667160589 2.490000e-85 327
5 TraesCS4A01G195900 chr4A 76.394 538 115 9 7710 8243 478192286 478192815 7.070000e-71 279
6 TraesCS4A01G195900 chr3B 99.004 5019 48 2 2693 7709 793111294 793116312 0.000000e+00 8990
7 TraesCS4A01G195900 chr3B 98.936 188 2 0 2269 2456 735978177 735978364 4.130000e-88 337
8 TraesCS4A01G195900 chr3B 96.020 201 5 3 2258 2456 819866778 819866977 3.220000e-84 324
9 TraesCS4A01G195900 chr5B 98.984 5020 49 2 2693 7710 257005864 257010883 0.000000e+00 8986
10 TraesCS4A01G195900 chr5B 98.944 5019 51 2 2693 7709 337169296 337174314 0.000000e+00 8973
11 TraesCS4A01G195900 chr5B 97.917 192 4 0 2268 2459 459179557 459179366 5.350000e-87 333
12 TraesCS4A01G195900 chr1A 98.984 5019 49 2 2693 7709 590339991 590334973 0.000000e+00 8985
13 TraesCS4A01G195900 chr1A 98.925 5021 51 3 2693 7711 548581849 548576830 0.000000e+00 8970
14 TraesCS4A01G195900 chr1A 98.886 5025 52 3 2693 7713 490790539 490785515 0.000000e+00 8966
15 TraesCS4A01G195900 chr1A 84.433 1394 172 22 900 2267 463218522 463219896 0.000000e+00 1330
16 TraesCS4A01G195900 chr1A 96.296 567 20 1 1 566 272747765 272748331 0.000000e+00 929
17 TraesCS4A01G195900 chr1A 96.106 565 21 1 3 566 403715474 403716038 0.000000e+00 920
18 TraesCS4A01G195900 chr1B 98.944 5021 49 3 2693 7709 510834179 510839199 0.000000e+00 8975
19 TraesCS4A01G195900 chr1B 85.900 1383 152 18 911 2268 487405524 487406888 0.000000e+00 1434
20 TraesCS4A01G195900 chr1B 79.892 925 135 26 7710 8618 487406884 487407773 1.690000e-176 630
21 TraesCS4A01G195900 chr1B 98.429 191 3 0 2269 2459 487930218 487930028 4.130000e-88 337
22 TraesCS4A01G195900 chr1B 97.927 193 2 1 2267 2459 343954644 343954834 5.350000e-87 333
23 TraesCS4A01G195900 chr4B 98.944 5020 50 3 2693 7709 545463362 545458343 0.000000e+00 8973
24 TraesCS4A01G195900 chr4B 96.721 1403 37 7 874 2268 139549317 139547916 0.000000e+00 2327
25 TraesCS4A01G195900 chr4B 86.027 1689 171 43 600 2268 139572539 139570896 0.000000e+00 1751
26 TraesCS4A01G195900 chr4B 97.174 920 25 1 7710 8628 139547920 139547001 0.000000e+00 1554
27 TraesCS4A01G195900 chr4B 79.310 1218 162 47 7710 8890 139570900 139569736 0.000000e+00 771
28 TraesCS4A01G195900 chr4B 88.449 632 29 10 8612 9240 139546988 139546398 0.000000e+00 723
29 TraesCS4A01G195900 chr2A 98.924 5019 52 2 2693 7709 54697275 54702293 0.000000e+00 8968
30 TraesCS4A01G195900 chr4D 95.082 1403 43 15 874 2268 97962536 97961152 0.000000e+00 2185
31 TraesCS4A01G195900 chr4D 87.389 1356 127 19 919 2268 97970264 97968947 0.000000e+00 1517
32 TraesCS4A01G195900 chr4D 96.778 869 25 3 7710 8577 97961156 97960290 0.000000e+00 1447
33 TraesCS4A01G195900 chr4D 80.952 882 143 17 1401 2268 98015418 98014548 0.000000e+00 675
34 TraesCS4A01G195900 chr4D 86.935 620 44 28 8630 9240 97960308 97959717 0.000000e+00 662
35 TraesCS4A01G195900 chr4D 83.784 666 80 17 7710 8372 97968951 97968311 2.850000e-169 606
36 TraesCS4A01G195900 chr4D 77.079 541 112 9 7710 8246 98014552 98014020 1.510000e-77 302
37 TraesCS4A01G195900 chr4D 80.000 350 64 4 7855 8203 435197777 435197433 4.280000e-63 254
38 TraesCS4A01G195900 chr4D 79.817 327 45 14 600 923 97971586 97971278 1.560000e-52 219
39 TraesCS4A01G195900 chr1D 86.136 1320 145 17 969 2268 363861164 363862465 0.000000e+00 1389
40 TraesCS4A01G195900 chr1D 80.607 923 136 23 7710 8620 363862461 363863352 0.000000e+00 673
41 TraesCS4A01G195900 chr3A 95.812 573 22 2 3 573 196844918 196845490 0.000000e+00 924
42 TraesCS4A01G195900 chr3A 95.767 567 23 1 1 566 478508836 478509402 0.000000e+00 913
43 TraesCS4A01G195900 chr3A 98.438 192 2 1 2269 2459 701744061 701744252 4.130000e-88 337
44 TraesCS4A01G195900 chr5A 96.113 566 21 1 1 565 289465638 289465073 0.000000e+00 922
45 TraesCS4A01G195900 chr5A 96.099 564 21 1 3 565 122588432 122587869 0.000000e+00 918
46 TraesCS4A01G195900 chr5A 95.929 565 22 1 3 566 360793278 360793842 0.000000e+00 915
47 TraesCS4A01G195900 chr7A 95.936 566 22 1 1 565 545341204 545341769 0.000000e+00 917
48 TraesCS4A01G195900 chr6B 77.729 1365 216 48 933 2268 134838234 134839539 0.000000e+00 756
49 TraesCS4A01G195900 chr6D 78.814 708 89 30 932 1632 61002875 61003528 3.990000e-113 420
50 TraesCS4A01G195900 chr6A 98.429 191 3 0 2269 2459 569696533 569696723 4.130000e-88 337
51 TraesCS4A01G195900 chr2B 97.949 195 1 2 2266 2459 36889494 36889686 1.490000e-87 335


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 TraesCS4A01G195900 chr4A 478208590 478217829 9239 False 8317.000000 12092 100.000000 1 9240 2 chr4A.!!$F4 9239
1 TraesCS4A01G195900 chr4A 213953170 213953733 563 False 918.000000 918 96.099000 3 565 1 chr4A.!!$F1 562
2 TraesCS4A01G195900 chr4A 478191411 478192815 1404 False 484.000000 689 78.794000 1401 8243 2 chr4A.!!$F3 6842
3 TraesCS4A01G195900 chr3B 793111294 793116312 5018 False 8990.000000 8990 99.004000 2693 7709 1 chr3B.!!$F2 5016
4 TraesCS4A01G195900 chr5B 257005864 257010883 5019 False 8986.000000 8986 98.984000 2693 7710 1 chr5B.!!$F1 5017
5 TraesCS4A01G195900 chr5B 337169296 337174314 5018 False 8973.000000 8973 98.944000 2693 7709 1 chr5B.!!$F2 5016
6 TraesCS4A01G195900 chr1A 590334973 590339991 5018 True 8985.000000 8985 98.984000 2693 7709 1 chr1A.!!$R3 5016
7 TraesCS4A01G195900 chr1A 548576830 548581849 5019 True 8970.000000 8970 98.925000 2693 7711 1 chr1A.!!$R2 5018
8 TraesCS4A01G195900 chr1A 490785515 490790539 5024 True 8966.000000 8966 98.886000 2693 7713 1 chr1A.!!$R1 5020
9 TraesCS4A01G195900 chr1A 463218522 463219896 1374 False 1330.000000 1330 84.433000 900 2267 1 chr1A.!!$F3 1367
10 TraesCS4A01G195900 chr1A 272747765 272748331 566 False 929.000000 929 96.296000 1 566 1 chr1A.!!$F1 565
11 TraesCS4A01G195900 chr1A 403715474 403716038 564 False 920.000000 920 96.106000 3 566 1 chr1A.!!$F2 563
12 TraesCS4A01G195900 chr1B 510834179 510839199 5020 False 8975.000000 8975 98.944000 2693 7709 1 chr1B.!!$F2 5016
13 TraesCS4A01G195900 chr1B 487405524 487407773 2249 False 1032.000000 1434 82.896000 911 8618 2 chr1B.!!$F3 7707
14 TraesCS4A01G195900 chr4B 545458343 545463362 5019 True 8973.000000 8973 98.944000 2693 7709 1 chr4B.!!$R1 5016
15 TraesCS4A01G195900 chr4B 139546398 139549317 2919 True 1534.666667 2327 94.114667 874 9240 3 chr4B.!!$R2 8366
16 TraesCS4A01G195900 chr4B 139569736 139572539 2803 True 1261.000000 1751 82.668500 600 8890 2 chr4B.!!$R3 8290
17 TraesCS4A01G195900 chr2A 54697275 54702293 5018 False 8968.000000 8968 98.924000 2693 7709 1 chr2A.!!$F1 5016
18 TraesCS4A01G195900 chr4D 97959717 97962536 2819 True 1431.333333 2185 92.931667 874 9240 3 chr4D.!!$R2 8366
19 TraesCS4A01G195900 chr4D 97968311 97971586 3275 True 780.666667 1517 83.663333 600 8372 3 chr4D.!!$R3 7772
20 TraesCS4A01G195900 chr4D 98014020 98015418 1398 True 488.500000 675 79.015500 1401 8246 2 chr4D.!!$R4 6845
21 TraesCS4A01G195900 chr1D 363861164 363863352 2188 False 1031.000000 1389 83.371500 969 8620 2 chr1D.!!$F1 7651
22 TraesCS4A01G195900 chr3A 196844918 196845490 572 False 924.000000 924 95.812000 3 573 1 chr3A.!!$F1 570
23 TraesCS4A01G195900 chr3A 478508836 478509402 566 False 913.000000 913 95.767000 1 566 1 chr3A.!!$F2 565
24 TraesCS4A01G195900 chr5A 289465073 289465638 565 True 922.000000 922 96.113000 1 565 1 chr5A.!!$R2 564
25 TraesCS4A01G195900 chr5A 122587869 122588432 563 True 918.000000 918 96.099000 3 565 1 chr5A.!!$R1 562
26 TraesCS4A01G195900 chr5A 360793278 360793842 564 False 915.000000 915 95.929000 3 566 1 chr5A.!!$F1 563
27 TraesCS4A01G195900 chr7A 545341204 545341769 565 False 917.000000 917 95.936000 1 565 1 chr7A.!!$F1 564
28 TraesCS4A01G195900 chr6B 134838234 134839539 1305 False 756.000000 756 77.729000 933 2268 1 chr6B.!!$F1 1335
29 TraesCS4A01G195900 chr6D 61002875 61003528 653 False 420.000000 420 78.814000 932 1632 1 chr6D.!!$F1 700

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
570 572 0.591170 CCAGAACGCCGACAAACAAT 59.409 50.000 0.00 0.00 0.00 2.71 F
888 894 1.004745 TCTCTGGACATTTGGGCCTTC 59.995 52.381 4.53 0.00 0.00 3.46 F
2365 3463 0.690762 TAGAGGGTTGTGCCAGTTCC 59.309 55.000 0.00 0.00 39.65 3.62 F
2426 3524 0.167470 GTCCGCTTCCGCCTAAAAAC 59.833 55.000 0.00 0.00 0.00 2.43 F
3198 4296 0.179020 CCTCCTGTGCTGGTTGACAA 60.179 55.000 0.00 0.00 0.00 3.18 F
3200 4298 0.254462 TCCTGTGCTGGTTGACAACA 59.746 50.000 19.58 5.62 0.00 3.33 F
3210 4308 0.944386 GTTGACAACATGCACGGTCT 59.056 50.000 13.52 0.00 0.00 3.85 F
3588 4686 1.064166 CAATGAGAGGGGCAACTCCAT 60.064 52.381 5.01 5.94 38.59 3.41 F
5278 6378 1.228769 TGTCCACTACCGAGCCACT 60.229 57.895 0.00 0.00 0.00 4.00 F
5356 6456 4.473196 TCCTCTATTGTTGCCTAACCATGA 59.527 41.667 0.00 0.00 35.92 3.07 F
6829 7930 2.423538 GGATGCTTAAGTGCAAACCGAT 59.576 45.455 4.02 0.00 46.61 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 3430 0.191064 CCTCTAGGGGTGGCCTATCA 59.809 60.000 3.32 0.00 0.00 2.15 R
2398 3496 0.248377 CGGAAGCGGACGTAACCTAG 60.248 60.000 0.00 0.00 0.00 3.02 R
3834 4932 0.034059 CTTGTGACACTTCGAGGCCT 59.966 55.000 3.86 3.86 0.00 5.19 R
3960 5058 2.958818 TGGAGTAGGACTGAGTGTGTT 58.041 47.619 0.00 0.00 0.00 3.32 R
4897 5997 1.478654 GGGCCAAAAGAGTCAGACCAA 60.479 52.381 4.39 0.00 0.00 3.67 R
5176 6276 3.118261 ACGATTAGTGGGCACATGAAGAT 60.118 43.478 0.00 0.00 0.00 2.40 R
5278 6378 3.959293 ACAGAGGATGAATGCATGACAA 58.041 40.909 0.00 0.00 34.11 3.18 R
5356 6456 2.359107 CACGACCAGTGCCTGCAT 60.359 61.111 0.00 0.00 44.72 3.96 R
6190 7291 2.242965 TCAATGGACCCATCAGAATGCT 59.757 45.455 1.48 0.00 35.31 3.79 R
7309 8410 2.441750 GGAGGCTGTGATTGGGGTATAA 59.558 50.000 0.00 0.00 0.00 0.98 R
8714 9886 1.202405 GCCCCAATAATTGACTTGCCG 60.202 52.381 0.00 0.00 0.00 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
132 133 2.299297 CCTGACTAAAGTTGGTCCTCGT 59.701 50.000 5.25 0.00 37.82 4.18
181 182 2.242043 CTTGGGCTCCACAATGACTTT 58.758 47.619 0.00 0.00 30.78 2.66
257 258 3.965539 ATGCTCTCGCCTGCGCTTT 62.966 57.895 9.73 0.00 39.59 3.51
274 275 2.158971 GCTTTCTCCCTTTGCACCAAAA 60.159 45.455 0.00 0.00 32.75 2.44
369 370 0.912487 TGAGGTACCCCGCCTTGATT 60.912 55.000 8.74 0.00 36.29 2.57
374 375 1.209747 GTACCCCGCCTTGATTTCTCT 59.790 52.381 0.00 0.00 0.00 3.10
512 514 4.660938 GCCCCCTTTGAGCCACGT 62.661 66.667 0.00 0.00 0.00 4.49
566 568 1.146485 TTCCCAGAACGCCGACAAA 59.854 52.632 0.00 0.00 0.00 2.83
567 569 1.161563 TTCCCAGAACGCCGACAAAC 61.162 55.000 0.00 0.00 0.00 2.93
568 570 1.890041 CCCAGAACGCCGACAAACA 60.890 57.895 0.00 0.00 0.00 2.83
569 571 1.440938 CCCAGAACGCCGACAAACAA 61.441 55.000 0.00 0.00 0.00 2.83
570 572 0.591170 CCAGAACGCCGACAAACAAT 59.409 50.000 0.00 0.00 0.00 2.71
571 573 1.801771 CCAGAACGCCGACAAACAATA 59.198 47.619 0.00 0.00 0.00 1.90
572 574 2.418628 CCAGAACGCCGACAAACAATAT 59.581 45.455 0.00 0.00 0.00 1.28
573 575 3.485216 CCAGAACGCCGACAAACAATATC 60.485 47.826 0.00 0.00 0.00 1.63
574 576 3.124466 CAGAACGCCGACAAACAATATCA 59.876 43.478 0.00 0.00 0.00 2.15
575 577 3.749088 AGAACGCCGACAAACAATATCAA 59.251 39.130 0.00 0.00 0.00 2.57
576 578 3.465122 ACGCCGACAAACAATATCAAC 57.535 42.857 0.00 0.00 0.00 3.18
577 579 2.809119 ACGCCGACAAACAATATCAACA 59.191 40.909 0.00 0.00 0.00 3.33
578 580 3.160545 CGCCGACAAACAATATCAACAC 58.839 45.455 0.00 0.00 0.00 3.32
579 581 3.364465 CGCCGACAAACAATATCAACACA 60.364 43.478 0.00 0.00 0.00 3.72
580 582 4.671508 CGCCGACAAACAATATCAACACAT 60.672 41.667 0.00 0.00 0.00 3.21
581 583 5.160641 GCCGACAAACAATATCAACACATT 58.839 37.500 0.00 0.00 0.00 2.71
582 584 5.633182 GCCGACAAACAATATCAACACATTT 59.367 36.000 0.00 0.00 0.00 2.32
583 585 6.145371 GCCGACAAACAATATCAACACATTTT 59.855 34.615 0.00 0.00 0.00 1.82
584 586 7.327275 GCCGACAAACAATATCAACACATTTTA 59.673 33.333 0.00 0.00 0.00 1.52
585 587 9.186323 CCGACAAACAATATCAACACATTTTAA 57.814 29.630 0.00 0.00 0.00 1.52
654 656 6.982141 TCATGATGAAATTTTGCAAGCTATCC 59.018 34.615 0.00 0.00 0.00 2.59
656 658 6.880484 TGATGAAATTTTGCAAGCTATCCAT 58.120 32.000 0.00 0.86 0.00 3.41
682 685 7.536895 TTTTTGTCAATGTTCCACATGAAAG 57.463 32.000 0.00 0.00 37.97 2.62
683 686 4.852134 TGTCAATGTTCCACATGAAAGG 57.148 40.909 0.00 0.00 37.97 3.11
688 691 6.587608 GTCAATGTTCCACATGAAAGGAATTC 59.412 38.462 17.45 0.00 44.98 2.17
720 724 9.830975 ATTTTTATTTTACTGTTCACCAAGCTT 57.169 25.926 0.00 0.00 0.00 3.74
722 726 9.738832 TTTTATTTTACTGTTCACCAAGCTTAC 57.261 29.630 0.00 0.00 0.00 2.34
723 727 6.952773 ATTTTACTGTTCACCAAGCTTACA 57.047 33.333 0.00 0.00 0.00 2.41
724 728 6.952773 TTTTACTGTTCACCAAGCTTACAT 57.047 33.333 0.00 0.00 0.00 2.29
725 729 5.940192 TTACTGTTCACCAAGCTTACATG 57.060 39.130 0.00 0.00 0.00 3.21
726 730 4.085357 ACTGTTCACCAAGCTTACATGA 57.915 40.909 0.00 0.02 0.00 3.07
727 731 4.067896 ACTGTTCACCAAGCTTACATGAG 58.932 43.478 0.00 0.00 0.00 2.90
728 732 2.813754 TGTTCACCAAGCTTACATGAGC 59.186 45.455 0.00 6.19 43.02 4.26
742 746 2.103263 ACATGAGCCTCGGGATTAGAAC 59.897 50.000 0.00 0.00 0.00 3.01
754 758 4.377022 CGGGATTAGAACAACACTTTCGTG 60.377 45.833 0.00 0.00 46.63 4.35
814 820 7.828508 AATTATACACTATACACCCGAGTCA 57.171 36.000 0.00 0.00 0.00 3.41
816 822 3.083122 ACACTATACACCCGAGTCACT 57.917 47.619 0.00 0.00 0.00 3.41
819 825 3.015327 ACTATACACCCGAGTCACTGAC 58.985 50.000 0.38 0.38 0.00 3.51
820 826 2.217510 ATACACCCGAGTCACTGACT 57.782 50.000 11.69 11.69 46.42 3.41
821 827 2.865119 TACACCCGAGTCACTGACTA 57.135 50.000 11.84 0.00 43.53 2.59
822 828 1.535833 ACACCCGAGTCACTGACTAG 58.464 55.000 11.84 11.56 43.53 2.57
823 829 1.202903 ACACCCGAGTCACTGACTAGT 60.203 52.381 11.84 7.32 43.53 2.57
824 830 1.887198 CACCCGAGTCACTGACTAGTT 59.113 52.381 11.84 0.00 43.53 2.24
825 831 2.296471 CACCCGAGTCACTGACTAGTTT 59.704 50.000 11.84 0.00 43.53 2.66
826 832 2.963782 ACCCGAGTCACTGACTAGTTTT 59.036 45.455 11.84 0.00 43.53 2.43
827 833 3.387050 ACCCGAGTCACTGACTAGTTTTT 59.613 43.478 11.84 0.00 43.53 1.94
869 875 1.208293 CTAGTGGGCTTTGAGAGGGTC 59.792 57.143 0.00 0.00 0.00 4.46
888 894 1.004745 TCTCTGGACATTTGGGCCTTC 59.995 52.381 4.53 0.00 0.00 3.46
1422 2467 4.386951 CCACCGTGTCCCGCATCA 62.387 66.667 0.00 0.00 34.38 3.07
1676 2744 2.047655 CCGAGCGCCACCTGTTTA 60.048 61.111 2.29 0.00 0.00 2.01
1739 2807 3.522750 AGAGCAAGGATCTGGACTTCATT 59.477 43.478 0.00 0.00 0.00 2.57
1794 2862 8.710749 TTATATCCATGGGAATCTTTTCAAGG 57.289 34.615 13.02 0.00 34.34 3.61
1813 2881 2.367567 AGGTTAGTCTTCGCCTTGTCAA 59.632 45.455 0.00 0.00 0.00 3.18
1837 2906 1.741770 GCCTCCGTGCGTGAAGATT 60.742 57.895 0.00 0.00 0.00 2.40
2267 3365 1.879380 TGCTTTCCCAATGTTGAGACG 59.121 47.619 0.00 0.00 0.00 4.18
2268 3366 1.880027 GCTTTCCCAATGTTGAGACGT 59.120 47.619 0.00 0.00 0.00 4.34
2269 3367 2.350772 GCTTTCCCAATGTTGAGACGTG 60.351 50.000 0.00 0.00 0.00 4.49
2270 3368 2.631160 TTCCCAATGTTGAGACGTGT 57.369 45.000 0.00 0.00 0.00 4.49
2271 3369 2.631160 TCCCAATGTTGAGACGTGTT 57.369 45.000 0.00 0.00 0.00 3.32
2272 3370 3.755112 TCCCAATGTTGAGACGTGTTA 57.245 42.857 0.00 0.00 0.00 2.41
2273 3371 3.659786 TCCCAATGTTGAGACGTGTTAG 58.340 45.455 0.00 0.00 0.00 2.34
2274 3372 3.322541 TCCCAATGTTGAGACGTGTTAGA 59.677 43.478 0.00 0.00 0.00 2.10
2275 3373 3.432252 CCCAATGTTGAGACGTGTTAGAC 59.568 47.826 0.00 0.00 0.00 2.59
2276 3374 4.307432 CCAATGTTGAGACGTGTTAGACT 58.693 43.478 0.00 0.00 0.00 3.24
2277 3375 4.150627 CCAATGTTGAGACGTGTTAGACTG 59.849 45.833 0.00 0.00 0.00 3.51
2278 3376 4.585955 ATGTTGAGACGTGTTAGACTGT 57.414 40.909 0.00 0.00 0.00 3.55
2279 3377 5.700722 ATGTTGAGACGTGTTAGACTGTA 57.299 39.130 0.00 0.00 0.00 2.74
2280 3378 5.700722 TGTTGAGACGTGTTAGACTGTAT 57.299 39.130 0.00 0.00 0.00 2.29
2281 3379 6.080648 TGTTGAGACGTGTTAGACTGTATT 57.919 37.500 0.00 0.00 0.00 1.89
2282 3380 6.509656 TGTTGAGACGTGTTAGACTGTATTT 58.490 36.000 0.00 0.00 0.00 1.40
2283 3381 7.650890 TGTTGAGACGTGTTAGACTGTATTTA 58.349 34.615 0.00 0.00 0.00 1.40
2284 3382 7.592533 TGTTGAGACGTGTTAGACTGTATTTAC 59.407 37.037 0.00 0.00 0.00 2.01
2285 3383 7.205737 TGAGACGTGTTAGACTGTATTTACA 57.794 36.000 0.00 0.00 34.56 2.41
2286 3384 7.823665 TGAGACGTGTTAGACTGTATTTACAT 58.176 34.615 0.00 0.00 35.36 2.29
2287 3385 7.753580 TGAGACGTGTTAGACTGTATTTACATG 59.246 37.037 0.00 0.00 35.36 3.21
2288 3386 7.600065 AGACGTGTTAGACTGTATTTACATGT 58.400 34.615 2.69 2.69 38.16 3.21
2289 3387 7.541091 AGACGTGTTAGACTGTATTTACATGTG 59.459 37.037 9.11 0.00 36.27 3.21
2290 3388 7.149973 ACGTGTTAGACTGTATTTACATGTGT 58.850 34.615 9.11 0.00 35.21 3.72
2291 3389 8.298854 ACGTGTTAGACTGTATTTACATGTGTA 58.701 33.333 9.11 0.00 35.21 2.90
2292 3390 9.297586 CGTGTTAGACTGTATTTACATGTGTAT 57.702 33.333 9.11 4.21 35.36 2.29
2345 3443 7.814693 ATATATATATGTGATAGGCCACCCC 57.185 40.000 5.01 0.00 36.26 4.95
2362 3460 2.377136 CCTAGAGGGTTGTGCCAGT 58.623 57.895 0.00 0.00 39.65 4.00
2363 3461 0.693049 CCTAGAGGGTTGTGCCAGTT 59.307 55.000 0.00 0.00 39.65 3.16
2364 3462 1.339151 CCTAGAGGGTTGTGCCAGTTC 60.339 57.143 0.00 0.00 39.65 3.01
2365 3463 0.690762 TAGAGGGTTGTGCCAGTTCC 59.309 55.000 0.00 0.00 39.65 3.62
2366 3464 1.603739 GAGGGTTGTGCCAGTTCCC 60.604 63.158 0.00 0.00 39.65 3.97
2367 3465 2.600470 GGGTTGTGCCAGTTCCCC 60.600 66.667 0.00 0.00 39.65 4.81
2368 3466 2.600470 GGTTGTGCCAGTTCCCCC 60.600 66.667 0.00 0.00 37.17 5.40
2384 3482 2.532250 CCCCCAAAGCCTATTGTCTT 57.468 50.000 0.00 0.00 0.00 3.01
2385 3483 3.662759 CCCCCAAAGCCTATTGTCTTA 57.337 47.619 0.00 0.00 0.00 2.10
2386 3484 3.288092 CCCCCAAAGCCTATTGTCTTAC 58.712 50.000 0.00 0.00 0.00 2.34
2387 3485 3.308832 CCCCCAAAGCCTATTGTCTTACA 60.309 47.826 0.00 0.00 0.00 2.41
2388 3486 4.536765 CCCCAAAGCCTATTGTCTTACAT 58.463 43.478 0.00 0.00 0.00 2.29
2389 3487 4.339247 CCCCAAAGCCTATTGTCTTACATG 59.661 45.833 0.00 0.00 0.00 3.21
2390 3488 4.339247 CCCAAAGCCTATTGTCTTACATGG 59.661 45.833 0.00 0.00 0.00 3.66
2391 3489 4.949856 CCAAAGCCTATTGTCTTACATGGT 59.050 41.667 0.00 0.00 0.00 3.55
2392 3490 6.119536 CCAAAGCCTATTGTCTTACATGGTA 58.880 40.000 0.00 0.00 0.00 3.25
2393 3491 6.772716 CCAAAGCCTATTGTCTTACATGGTAT 59.227 38.462 0.00 0.00 0.00 2.73
2394 3492 7.041098 CCAAAGCCTATTGTCTTACATGGTATC 60.041 40.741 0.00 0.00 0.00 2.24
2395 3493 6.747414 AGCCTATTGTCTTACATGGTATCA 57.253 37.500 0.00 0.00 0.00 2.15
2396 3494 6.525629 AGCCTATTGTCTTACATGGTATCAC 58.474 40.000 0.00 0.00 0.00 3.06
2397 3495 5.405571 GCCTATTGTCTTACATGGTATCACG 59.594 44.000 0.00 0.00 0.00 4.35
2398 3496 5.405571 CCTATTGTCTTACATGGTATCACGC 59.594 44.000 0.00 0.00 0.00 5.34
2399 3497 4.465632 TTGTCTTACATGGTATCACGCT 57.534 40.909 0.00 0.00 0.00 5.07
2400 3498 5.585820 TTGTCTTACATGGTATCACGCTA 57.414 39.130 0.00 0.00 0.00 4.26
2401 3499 5.183014 TGTCTTACATGGTATCACGCTAG 57.817 43.478 0.00 0.00 0.00 3.42
2402 3500 4.037565 TGTCTTACATGGTATCACGCTAGG 59.962 45.833 0.00 0.00 0.00 3.02
2403 3501 4.037684 GTCTTACATGGTATCACGCTAGGT 59.962 45.833 0.00 0.00 0.00 3.08
2404 3502 4.647853 TCTTACATGGTATCACGCTAGGTT 59.352 41.667 0.00 0.00 0.00 3.50
2405 3503 5.829391 TCTTACATGGTATCACGCTAGGTTA 59.171 40.000 0.00 0.00 0.00 2.85
2406 3504 4.317671 ACATGGTATCACGCTAGGTTAC 57.682 45.455 0.00 0.00 0.00 2.50
2407 3505 3.243301 ACATGGTATCACGCTAGGTTACG 60.243 47.826 0.00 0.00 0.00 3.18
2408 3506 2.368439 TGGTATCACGCTAGGTTACGT 58.632 47.619 0.00 0.00 44.75 3.57
2409 3507 2.355756 TGGTATCACGCTAGGTTACGTC 59.644 50.000 0.00 0.00 41.32 4.34
2410 3508 2.287248 GGTATCACGCTAGGTTACGTCC 60.287 54.545 0.00 0.00 41.32 4.79
2411 3509 0.379669 ATCACGCTAGGTTACGTCCG 59.620 55.000 0.00 0.00 41.32 4.79
2412 3510 1.870901 CACGCTAGGTTACGTCCGC 60.871 63.158 0.00 0.00 41.32 5.54
2413 3511 2.042831 ACGCTAGGTTACGTCCGCT 61.043 57.895 0.00 0.00 38.28 5.52
2414 3512 1.138247 CGCTAGGTTACGTCCGCTT 59.862 57.895 0.00 0.00 0.00 4.68
2415 3513 0.864797 CGCTAGGTTACGTCCGCTTC 60.865 60.000 0.00 0.00 0.00 3.86
2416 3514 0.527169 GCTAGGTTACGTCCGCTTCC 60.527 60.000 0.00 0.00 0.00 3.46
2417 3515 0.248377 CTAGGTTACGTCCGCTTCCG 60.248 60.000 0.00 0.00 0.00 4.30
2418 3516 2.270297 TAGGTTACGTCCGCTTCCGC 62.270 60.000 0.00 0.00 0.00 5.54
2419 3517 3.184003 GTTACGTCCGCTTCCGCC 61.184 66.667 0.00 0.00 0.00 6.13
2420 3518 3.376078 TTACGTCCGCTTCCGCCT 61.376 61.111 0.00 0.00 0.00 5.52
2421 3519 2.045708 TTACGTCCGCTTCCGCCTA 61.046 57.895 0.00 0.00 0.00 3.93
2422 3520 1.594194 TTACGTCCGCTTCCGCCTAA 61.594 55.000 0.00 0.00 0.00 2.69
2423 3521 1.594194 TACGTCCGCTTCCGCCTAAA 61.594 55.000 0.00 0.00 0.00 1.85
2424 3522 1.738830 CGTCCGCTTCCGCCTAAAA 60.739 57.895 0.00 0.00 0.00 1.52
2425 3523 1.293267 CGTCCGCTTCCGCCTAAAAA 61.293 55.000 0.00 0.00 0.00 1.94
2426 3524 0.167470 GTCCGCTTCCGCCTAAAAAC 59.833 55.000 0.00 0.00 0.00 2.43
2427 3525 0.956902 TCCGCTTCCGCCTAAAAACC 60.957 55.000 0.00 0.00 0.00 3.27
2428 3526 1.504900 CGCTTCCGCCTAAAAACCC 59.495 57.895 0.00 0.00 0.00 4.11
2429 3527 0.958876 CGCTTCCGCCTAAAAACCCT 60.959 55.000 0.00 0.00 0.00 4.34
2430 3528 1.676615 CGCTTCCGCCTAAAAACCCTA 60.677 52.381 0.00 0.00 0.00 3.53
2431 3529 2.439409 GCTTCCGCCTAAAAACCCTAA 58.561 47.619 0.00 0.00 0.00 2.69
2432 3530 2.821378 GCTTCCGCCTAAAAACCCTAAA 59.179 45.455 0.00 0.00 0.00 1.85
2433 3531 3.366679 GCTTCCGCCTAAAAACCCTAAAC 60.367 47.826 0.00 0.00 0.00 2.01
2434 3532 2.794103 TCCGCCTAAAAACCCTAAACC 58.206 47.619 0.00 0.00 0.00 3.27
2435 3533 1.469703 CCGCCTAAAAACCCTAAACCG 59.530 52.381 0.00 0.00 0.00 4.44
2436 3534 1.135603 CGCCTAAAAACCCTAAACCGC 60.136 52.381 0.00 0.00 0.00 5.68
2437 3535 1.203052 GCCTAAAAACCCTAAACCGCC 59.797 52.381 0.00 0.00 0.00 6.13
2438 3536 1.469703 CCTAAAAACCCTAAACCGCCG 59.530 52.381 0.00 0.00 0.00 6.46
2439 3537 0.880441 TAAAAACCCTAAACCGCCGC 59.120 50.000 0.00 0.00 0.00 6.53
2440 3538 1.808531 AAAAACCCTAAACCGCCGCC 61.809 55.000 0.00 0.00 0.00 6.13
3092 4190 1.338655 TCACCATCAAGTTGTCGTCGA 59.661 47.619 2.11 0.00 0.00 4.20
3114 4212 1.665679 CAATTACATCTTCTGGCGCGT 59.334 47.619 8.43 0.00 0.00 6.01
3186 4284 1.614824 CTCTCCCTTGCCCTCCTGT 60.615 63.158 0.00 0.00 0.00 4.00
3198 4296 0.179020 CCTCCTGTGCTGGTTGACAA 60.179 55.000 0.00 0.00 0.00 3.18
3200 4298 0.254462 TCCTGTGCTGGTTGACAACA 59.746 50.000 19.58 5.62 0.00 3.33
3210 4308 0.944386 GTTGACAACATGCACGGTCT 59.056 50.000 13.52 0.00 0.00 3.85
3267 4365 1.693627 GATCAGGCGAACCTCTCCTA 58.306 55.000 0.00 0.00 46.34 2.94
3588 4686 1.064166 CAATGAGAGGGGCAACTCCAT 60.064 52.381 5.01 5.94 38.59 3.41
3669 4767 3.781307 CCGATCCAGGGGCAACGA 61.781 66.667 0.00 0.00 37.60 3.85
3834 4932 3.071837 TGGTCGCGATGGGCACTA 61.072 61.111 14.06 0.00 43.84 2.74
3960 5058 4.704833 GCCGCAGAAGCCACAGGA 62.705 66.667 0.00 0.00 37.52 3.86
4897 5997 3.141398 AGCATCGTCACATTGTTGAAGT 58.859 40.909 0.00 0.00 0.00 3.01
5015 6115 6.464222 TCGTGTTTTGAATATGAAGACTCCT 58.536 36.000 0.00 0.00 0.00 3.69
5016 6116 6.368791 TCGTGTTTTGAATATGAAGACTCCTG 59.631 38.462 0.00 0.00 0.00 3.86
5278 6378 1.228769 TGTCCACTACCGAGCCACT 60.229 57.895 0.00 0.00 0.00 4.00
5356 6456 4.473196 TCCTCTATTGTTGCCTAACCATGA 59.527 41.667 0.00 0.00 35.92 3.07
6190 7291 6.070538 TCCAAATGGGTTTTCAAAGTGAAGAA 60.071 34.615 0.00 0.00 36.39 2.52
6464 7565 3.481453 CCCTGATCATCTCTGTCGTCTA 58.519 50.000 0.00 0.00 0.00 2.59
6829 7930 2.423538 GGATGCTTAAGTGCAAACCGAT 59.576 45.455 4.02 0.00 46.61 4.18
6865 7966 5.187772 TGTCTACCACTGATAAGCTCAATGT 59.812 40.000 0.00 0.00 28.95 2.71
7013 8114 3.134879 TCACCCCGTGACACTCAC 58.865 61.111 3.68 0.00 43.65 3.51
7309 8410 4.042187 ACAGTCCTTGCTTCAGGAGTTAAT 59.958 41.667 5.11 0.00 43.21 1.40
8205 9320 1.663135 GAACTTCAAGAGAGCATCGGC 59.337 52.381 0.00 0.00 42.67 5.54
8300 9415 5.250200 TGGAAGTTGTTGTGTTCTGTAGTT 58.750 37.500 0.00 0.00 0.00 2.24
8404 9540 4.153986 GTCTTCGTTGATGCAAATGACTG 58.846 43.478 0.00 0.00 0.00 3.51
8414 9550 2.629137 TGCAAATGACTGCCATTCTGTT 59.371 40.909 0.00 0.00 44.28 3.16
8520 9661 6.845302 TCTGATGAGAATTACATTGCACAAC 58.155 36.000 0.00 0.00 0.00 3.32
8556 9697 1.384191 GAGGCTTGATGTTGGGGGT 59.616 57.895 0.00 0.00 0.00 4.95
8594 9737 5.948162 ACAGCTGAGATAATCCATGTTTTGT 59.052 36.000 23.35 0.00 0.00 2.83
8651 9823 2.760092 GGATATTTGTTCCAGCTGGCAA 59.240 45.455 28.91 23.05 33.21 4.52
8762 9934 1.755179 ATGGCCAATCTGGTTCTTCG 58.245 50.000 10.96 0.00 40.46 3.79
8763 9935 0.690192 TGGCCAATCTGGTTCTTCGA 59.310 50.000 0.61 0.00 40.46 3.71
8771 9943 7.321963 CCAATCTGGTTCTTCGATTGCGAAA 62.322 44.000 0.00 0.00 43.31 3.46
8814 9987 5.059833 AGCCAATTTGGTTATTTTCGCAAA 58.940 33.333 16.62 0.00 40.46 3.68
8871 10058 3.097614 ACGCCTAAGAATAGTGTGTCCT 58.902 45.455 0.00 0.00 0.00 3.85
8905 10092 3.857549 TGATACGCAGCATCCTAGATC 57.142 47.619 0.00 0.00 0.00 2.75
8906 10093 3.157087 TGATACGCAGCATCCTAGATCA 58.843 45.455 0.00 0.00 0.00 2.92
8907 10094 3.192212 TGATACGCAGCATCCTAGATCAG 59.808 47.826 0.00 0.00 0.00 2.90
8908 10095 1.407936 ACGCAGCATCCTAGATCAGT 58.592 50.000 0.00 0.00 0.00 3.41
8909 10096 1.759445 ACGCAGCATCCTAGATCAGTT 59.241 47.619 0.00 0.00 0.00 3.16
8910 10097 2.959030 ACGCAGCATCCTAGATCAGTTA 59.041 45.455 0.00 0.00 0.00 2.24
8911 10098 3.243569 ACGCAGCATCCTAGATCAGTTAC 60.244 47.826 0.00 0.00 0.00 2.50
8912 10099 3.005261 CGCAGCATCCTAGATCAGTTACT 59.995 47.826 0.00 0.00 0.00 2.24
8913 10100 4.555262 GCAGCATCCTAGATCAGTTACTC 58.445 47.826 0.00 0.00 0.00 2.59
8914 10101 4.280677 GCAGCATCCTAGATCAGTTACTCT 59.719 45.833 0.00 0.00 0.00 3.24
8915 10102 5.221422 GCAGCATCCTAGATCAGTTACTCTT 60.221 44.000 0.00 0.00 0.00 2.85
8916 10103 6.685116 GCAGCATCCTAGATCAGTTACTCTTT 60.685 42.308 0.00 0.00 0.00 2.52
8917 10104 6.700960 CAGCATCCTAGATCAGTTACTCTTTG 59.299 42.308 0.00 0.00 0.00 2.77
8918 10105 5.465056 GCATCCTAGATCAGTTACTCTTTGC 59.535 44.000 0.00 0.00 0.00 3.68
8919 10106 6.685116 GCATCCTAGATCAGTTACTCTTTGCT 60.685 42.308 0.00 0.00 0.00 3.91
8920 10107 6.214191 TCCTAGATCAGTTACTCTTTGCTG 57.786 41.667 0.00 0.00 0.00 4.41
8921 10108 4.808364 CCTAGATCAGTTACTCTTTGCTGC 59.192 45.833 0.00 0.00 0.00 5.25
8922 10109 4.550076 AGATCAGTTACTCTTTGCTGCT 57.450 40.909 0.00 0.00 0.00 4.24
8923 10110 5.667539 AGATCAGTTACTCTTTGCTGCTA 57.332 39.130 0.00 0.00 0.00 3.49
8924 10111 5.659463 AGATCAGTTACTCTTTGCTGCTAG 58.341 41.667 0.00 0.00 0.00 3.42
8925 10112 3.589988 TCAGTTACTCTTTGCTGCTAGC 58.410 45.455 8.10 8.10 42.82 3.42
8926 10113 2.675348 CAGTTACTCTTTGCTGCTAGCC 59.325 50.000 13.29 0.00 41.51 3.93
8927 10114 2.569404 AGTTACTCTTTGCTGCTAGCCT 59.431 45.455 13.29 0.00 41.51 4.58
8956 10143 8.212995 TCCATTTATTCTATGATCTTCTGCACA 58.787 33.333 0.00 0.00 0.00 4.57
8975 10162 7.228507 TCTGCACACAATGATAAAGTAGTTGTT 59.771 33.333 0.00 0.00 31.19 2.83
8982 10169 8.349983 ACAATGATAAAGTAGTTGTTGTTCCAC 58.650 33.333 0.00 0.00 29.38 4.02
9037 10230 5.997385 TCTTCAGTTGCGAAAAATAAGGTC 58.003 37.500 0.00 0.00 0.00 3.85
9074 10267 4.202010 GCTGTAGGCTTTTCAGTTTTCACA 60.202 41.667 0.00 0.00 38.06 3.58
9084 10277 9.650371 GCTTTTCAGTTTTCACAAATAATTTCC 57.350 29.630 0.00 0.00 0.00 3.13
9088 10281 7.142680 TCAGTTTTCACAAATAATTTCCGACC 58.857 34.615 0.00 0.00 0.00 4.79
9111 10304 2.617658 AGAGACGGGGTAGACCTTTTT 58.382 47.619 0.00 0.00 40.03 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 5.269554 ACCAGATGTTCCCCTTCAAAATA 57.730 39.130 0.00 0.00 0.00 1.40
181 182 2.203788 AGTCCAACGGCAGGGAGA 60.204 61.111 0.00 0.00 32.85 3.71
257 258 2.038659 CCTTTTTGGTGCAAAGGGAGA 58.961 47.619 6.26 0.00 44.67 3.71
274 275 0.035458 CGCAGTGTCCTCCTTTCCTT 59.965 55.000 0.00 0.00 0.00 3.36
315 316 0.313672 GCAAGCCATGACGACCAAAA 59.686 50.000 0.00 0.00 0.00 2.44
369 370 2.361230 TCGCGAGGAGGCAGAGAA 60.361 61.111 3.71 0.00 0.00 2.87
413 414 2.049433 CGGACGACACGGAGCTTT 60.049 61.111 0.00 0.00 0.00 3.51
520 522 2.281970 CAGACTTGCCTGCCTGCA 60.282 61.111 0.00 0.00 40.07 4.41
632 634 6.283544 TGGATAGCTTGCAAAATTTCATCA 57.716 33.333 0.00 0.00 0.00 3.07
672 675 9.880157 AAAATAATCTGAATTCCTTTCATGTGG 57.120 29.630 2.27 0.00 43.30 4.17
694 698 9.830975 AAGCTTGGTGAACAGTAAAATAAAAAT 57.169 25.926 0.00 0.00 0.00 1.82
712 716 1.406069 CGAGGCTCATGTAAGCTTGGT 60.406 52.381 15.95 0.00 42.13 3.67
715 719 0.179000 CCCGAGGCTCATGTAAGCTT 59.821 55.000 15.95 3.48 42.13 3.74
716 720 0.687757 TCCCGAGGCTCATGTAAGCT 60.688 55.000 15.95 0.00 42.13 3.74
717 721 0.394565 ATCCCGAGGCTCATGTAAGC 59.605 55.000 15.95 0.00 41.73 3.09
718 722 2.918712 AATCCCGAGGCTCATGTAAG 57.081 50.000 15.95 0.00 0.00 2.34
719 723 3.572642 TCTAATCCCGAGGCTCATGTAA 58.427 45.455 15.95 0.00 0.00 2.41
720 724 3.238788 TCTAATCCCGAGGCTCATGTA 57.761 47.619 15.95 0.00 0.00 2.29
721 725 2.088104 TCTAATCCCGAGGCTCATGT 57.912 50.000 15.95 0.00 0.00 3.21
722 726 2.103094 TGTTCTAATCCCGAGGCTCATG 59.897 50.000 15.95 4.56 0.00 3.07
723 727 2.398588 TGTTCTAATCCCGAGGCTCAT 58.601 47.619 15.95 0.00 0.00 2.90
724 728 1.860641 TGTTCTAATCCCGAGGCTCA 58.139 50.000 15.95 0.00 0.00 4.26
725 729 2.093658 TGTTGTTCTAATCCCGAGGCTC 60.094 50.000 3.87 3.87 0.00 4.70
726 730 1.906574 TGTTGTTCTAATCCCGAGGCT 59.093 47.619 0.00 0.00 0.00 4.58
727 731 2.007608 GTGTTGTTCTAATCCCGAGGC 58.992 52.381 0.00 0.00 0.00 4.70
728 732 3.611766 AGTGTTGTTCTAATCCCGAGG 57.388 47.619 0.00 0.00 0.00 4.63
788 792 9.524496 TGACTCGGGTGTATAGTGTATAATTAT 57.476 33.333 0.00 2.97 0.00 1.28
790 794 7.504911 AGTGACTCGGGTGTATAGTGTATAATT 59.495 37.037 0.00 0.00 0.00 1.40
791 795 7.002879 AGTGACTCGGGTGTATAGTGTATAAT 58.997 38.462 0.00 0.00 0.00 1.28
825 831 5.067283 GTCAGTGACTCCTTTTGCCTAAAAA 59.933 40.000 16.26 0.00 35.50 1.94
826 832 4.578928 GTCAGTGACTCCTTTTGCCTAAAA 59.421 41.667 16.26 0.00 34.75 1.52
827 833 4.134563 GTCAGTGACTCCTTTTGCCTAAA 58.865 43.478 16.26 0.00 0.00 1.85
828 834 3.391296 AGTCAGTGACTCCTTTTGCCTAA 59.609 43.478 20.34 0.00 38.71 2.69
829 835 2.972713 AGTCAGTGACTCCTTTTGCCTA 59.027 45.455 20.34 0.00 38.71 3.93
830 836 1.771255 AGTCAGTGACTCCTTTTGCCT 59.229 47.619 20.34 0.00 38.71 4.75
831 837 2.262423 AGTCAGTGACTCCTTTTGCC 57.738 50.000 20.34 0.00 38.71 4.52
832 838 3.996480 ACTAGTCAGTGACTCCTTTTGC 58.004 45.455 28.70 0.00 42.40 3.68
857 863 2.251818 TGTCCAGAGACCCTCTCAAAG 58.748 52.381 2.20 0.00 45.73 2.77
869 875 1.467920 GAAGGCCCAAATGTCCAGAG 58.532 55.000 0.00 0.00 0.00 3.35
888 894 0.554792 ATTGCTCCTCATCCTTGGGG 59.445 55.000 0.00 0.00 45.89 4.96
896 903 3.526841 AGAGAAGGGAAATTGCTCCTCAT 59.473 43.478 0.00 0.00 35.63 2.90
898 905 3.643199 AGAGAAGGGAAATTGCTCCTC 57.357 47.619 0.00 0.00 35.63 3.71
1016 2045 2.595095 GATCCATGGGAACGGGCA 59.405 61.111 13.02 0.00 34.34 5.36
1407 2452 2.186903 GATGATGCGGGACACGGT 59.813 61.111 0.00 0.00 44.51 4.83
1571 2618 1.305046 GGTGGAGGGGAGAACGAGA 60.305 63.158 0.00 0.00 0.00 4.04
1676 2744 1.187087 CGAGCTCAAGGAGGTTAGGT 58.813 55.000 15.40 0.00 40.67 3.08
1739 2807 4.361971 ACGGGGCTCCTGTCGAGA 62.362 66.667 0.00 0.00 39.13 4.04
1813 2881 4.250305 ACGCACGGAGGCTTTGGT 62.250 61.111 0.00 0.00 0.00 3.67
1837 2906 5.567037 TTTCTTCAAAGGAGGACATGAGA 57.433 39.130 0.00 0.00 0.00 3.27
2095 3177 9.017509 TCAATGCACTCAATTAAGAGAAGAAAT 57.982 29.630 0.00 0.00 38.98 2.17
2319 3417 9.507381 GGGGTGGCCTATCACATATATATATAT 57.493 37.037 3.32 9.12 39.27 0.86
2320 3418 8.697529 AGGGGTGGCCTATCACATATATATATA 58.302 37.037 3.32 4.92 39.27 0.86
2321 3419 7.557283 AGGGGTGGCCTATCACATATATATAT 58.443 38.462 3.32 0.00 39.27 0.86
2322 3420 6.945371 AGGGGTGGCCTATCACATATATATA 58.055 40.000 3.32 0.00 39.27 0.86
2323 3421 5.804013 AGGGGTGGCCTATCACATATATAT 58.196 41.667 3.32 0.00 39.27 0.86
2324 3422 5.235003 AGGGGTGGCCTATCACATATATA 57.765 43.478 3.32 0.00 39.27 0.86
2325 3423 4.094216 AGGGGTGGCCTATCACATATAT 57.906 45.455 3.32 0.00 39.27 0.86
2326 3424 3.577968 AGGGGTGGCCTATCACATATA 57.422 47.619 3.32 0.00 39.27 0.86
2327 3425 2.440494 AGGGGTGGCCTATCACATAT 57.560 50.000 3.32 0.00 39.27 1.78
2328 3426 2.453212 TCTAGGGGTGGCCTATCACATA 59.547 50.000 3.32 0.00 39.27 2.29
2329 3427 1.223077 TCTAGGGGTGGCCTATCACAT 59.777 52.381 3.32 0.00 39.27 3.21
2330 3428 0.639943 TCTAGGGGTGGCCTATCACA 59.360 55.000 3.32 0.00 39.27 3.58
2331 3429 1.343069 CTCTAGGGGTGGCCTATCAC 58.657 60.000 3.32 0.00 36.95 3.06
2332 3430 0.191064 CCTCTAGGGGTGGCCTATCA 59.809 60.000 3.32 0.00 0.00 2.15
2333 3431 3.074788 CCTCTAGGGGTGGCCTATC 57.925 63.158 3.32 0.00 0.00 2.08
2344 3442 0.693049 AACTGGCACAACCCTCTAGG 59.307 55.000 0.00 0.00 38.70 3.02
2345 3443 1.339151 GGAACTGGCACAACCCTCTAG 60.339 57.143 0.00 0.00 38.70 2.43
2346 3444 0.690762 GGAACTGGCACAACCCTCTA 59.309 55.000 0.00 0.00 38.70 2.43
2347 3445 1.456287 GGAACTGGCACAACCCTCT 59.544 57.895 0.00 0.00 38.70 3.69
2348 3446 1.603739 GGGAACTGGCACAACCCTC 60.604 63.158 9.87 0.00 40.97 4.30
2349 3447 2.520968 GGGAACTGGCACAACCCT 59.479 61.111 9.87 0.00 40.97 4.34
2350 3448 2.600470 GGGGAACTGGCACAACCC 60.600 66.667 8.94 8.94 42.53 4.11
2351 3449 2.600470 GGGGGAACTGGCACAACC 60.600 66.667 0.00 0.00 38.70 3.77
2365 3463 2.532250 AAGACAATAGGCTTTGGGGG 57.468 50.000 0.00 0.00 0.00 5.40
2366 3464 3.963129 TGTAAGACAATAGGCTTTGGGG 58.037 45.455 0.00 0.00 0.00 4.96
2367 3465 4.339247 CCATGTAAGACAATAGGCTTTGGG 59.661 45.833 0.00 0.00 0.00 4.12
2368 3466 4.949856 ACCATGTAAGACAATAGGCTTTGG 59.050 41.667 0.00 0.00 0.00 3.28
2369 3467 7.498900 TGATACCATGTAAGACAATAGGCTTTG 59.501 37.037 0.00 0.00 0.00 2.77
2370 3468 7.499232 GTGATACCATGTAAGACAATAGGCTTT 59.501 37.037 0.00 0.00 0.00 3.51
2371 3469 6.992715 GTGATACCATGTAAGACAATAGGCTT 59.007 38.462 0.00 0.00 0.00 4.35
2372 3470 6.525629 GTGATACCATGTAAGACAATAGGCT 58.474 40.000 0.00 0.00 0.00 4.58
2373 3471 5.405571 CGTGATACCATGTAAGACAATAGGC 59.594 44.000 0.00 0.00 0.00 3.93
2374 3472 5.405571 GCGTGATACCATGTAAGACAATAGG 59.594 44.000 0.00 0.00 0.00 2.57
2375 3473 6.216569 AGCGTGATACCATGTAAGACAATAG 58.783 40.000 0.00 0.00 0.00 1.73
2376 3474 6.156748 AGCGTGATACCATGTAAGACAATA 57.843 37.500 0.00 0.00 0.00 1.90
2377 3475 5.023533 AGCGTGATACCATGTAAGACAAT 57.976 39.130 0.00 0.00 0.00 2.71
2378 3476 4.465632 AGCGTGATACCATGTAAGACAA 57.534 40.909 0.00 0.00 0.00 3.18
2379 3477 4.037565 CCTAGCGTGATACCATGTAAGACA 59.962 45.833 0.00 0.00 0.00 3.41
2380 3478 4.037684 ACCTAGCGTGATACCATGTAAGAC 59.962 45.833 0.00 0.00 0.00 3.01
2381 3479 4.212716 ACCTAGCGTGATACCATGTAAGA 58.787 43.478 0.00 0.00 0.00 2.10
2382 3480 4.585955 ACCTAGCGTGATACCATGTAAG 57.414 45.455 0.00 0.00 0.00 2.34
2383 3481 5.506151 CGTAACCTAGCGTGATACCATGTAA 60.506 44.000 0.00 0.00 0.00 2.41
2384 3482 4.023792 CGTAACCTAGCGTGATACCATGTA 60.024 45.833 0.00 0.00 0.00 2.29
2385 3483 3.243301 CGTAACCTAGCGTGATACCATGT 60.243 47.826 0.00 0.00 0.00 3.21
2386 3484 3.243301 ACGTAACCTAGCGTGATACCATG 60.243 47.826 0.00 0.00 40.03 3.66
2387 3485 2.954318 ACGTAACCTAGCGTGATACCAT 59.046 45.455 0.00 0.00 40.03 3.55
2388 3486 2.355756 GACGTAACCTAGCGTGATACCA 59.644 50.000 0.00 0.00 41.70 3.25
2389 3487 2.287248 GGACGTAACCTAGCGTGATACC 60.287 54.545 0.00 0.00 41.70 2.73
2390 3488 2.600792 CGGACGTAACCTAGCGTGATAC 60.601 54.545 0.00 0.00 41.70 2.24
2391 3489 1.599071 CGGACGTAACCTAGCGTGATA 59.401 52.381 0.00 0.00 41.70 2.15
2392 3490 0.379669 CGGACGTAACCTAGCGTGAT 59.620 55.000 0.00 0.00 41.70 3.06
2393 3491 1.796151 CGGACGTAACCTAGCGTGA 59.204 57.895 0.00 0.00 41.70 4.35
2394 3492 1.870901 GCGGACGTAACCTAGCGTG 60.871 63.158 0.00 0.00 41.70 5.34
2395 3493 1.589716 AAGCGGACGTAACCTAGCGT 61.590 55.000 0.00 0.00 44.50 5.07
2396 3494 0.864797 GAAGCGGACGTAACCTAGCG 60.865 60.000 0.00 0.00 0.00 4.26
2397 3495 0.527169 GGAAGCGGACGTAACCTAGC 60.527 60.000 0.00 0.00 0.00 3.42
2398 3496 0.248377 CGGAAGCGGACGTAACCTAG 60.248 60.000 0.00 0.00 0.00 3.02
2399 3497 1.802636 CGGAAGCGGACGTAACCTA 59.197 57.895 0.00 0.00 0.00 3.08
2400 3498 2.570181 CGGAAGCGGACGTAACCT 59.430 61.111 0.00 0.00 0.00 3.50
2412 3510 3.192001 GGTTTAGGGTTTTTAGGCGGAAG 59.808 47.826 0.00 0.00 0.00 3.46
2413 3511 3.156293 GGTTTAGGGTTTTTAGGCGGAA 58.844 45.455 0.00 0.00 0.00 4.30
2414 3512 2.794103 GGTTTAGGGTTTTTAGGCGGA 58.206 47.619 0.00 0.00 0.00 5.54
2415 3513 1.469703 CGGTTTAGGGTTTTTAGGCGG 59.530 52.381 0.00 0.00 0.00 6.13
2416 3514 1.135603 GCGGTTTAGGGTTTTTAGGCG 60.136 52.381 0.00 0.00 0.00 5.52
2417 3515 1.203052 GGCGGTTTAGGGTTTTTAGGC 59.797 52.381 0.00 0.00 0.00 3.93
2418 3516 1.469703 CGGCGGTTTAGGGTTTTTAGG 59.530 52.381 0.00 0.00 0.00 2.69
2419 3517 1.135603 GCGGCGGTTTAGGGTTTTTAG 60.136 52.381 9.78 0.00 0.00 1.85
2420 3518 0.880441 GCGGCGGTTTAGGGTTTTTA 59.120 50.000 9.78 0.00 0.00 1.52
2421 3519 1.661480 GCGGCGGTTTAGGGTTTTT 59.339 52.632 9.78 0.00 0.00 1.94
2422 3520 2.270257 GGCGGCGGTTTAGGGTTTT 61.270 57.895 9.78 0.00 0.00 2.43
2423 3521 2.674033 GGCGGCGGTTTAGGGTTT 60.674 61.111 9.78 0.00 0.00 3.27
3092 4190 2.095853 CGCGCCAGAAGATGTAATTGTT 59.904 45.455 0.00 0.00 0.00 2.83
3114 4212 0.108585 AAGAAGCGGAAGAACCTGCA 59.891 50.000 0.00 0.00 39.38 4.41
3186 4284 0.385029 GTGCATGTTGTCAACCAGCA 59.615 50.000 21.38 21.38 38.74 4.41
3198 4296 1.195115 ATAGACCAGACCGTGCATGT 58.805 50.000 4.96 0.00 0.00 3.21
3200 4298 3.006967 GGATTATAGACCAGACCGTGCAT 59.993 47.826 0.00 0.00 0.00 3.96
3210 4308 1.968493 GGTGAGCCGGATTATAGACCA 59.032 52.381 5.05 0.00 0.00 4.02
3267 4365 2.039624 AGAGCGACCCCTGGATGT 59.960 61.111 0.00 0.00 0.00 3.06
3834 4932 0.034059 CTTGTGACACTTCGAGGCCT 59.966 55.000 3.86 3.86 0.00 5.19
3960 5058 2.958818 TGGAGTAGGACTGAGTGTGTT 58.041 47.619 0.00 0.00 0.00 3.32
4444 5544 3.027412 ACACTAGGAAGCTCATGACGAT 58.973 45.455 0.00 0.00 0.00 3.73
4864 5964 4.392754 TGTGACGATGCTTACGTTCTACTA 59.607 41.667 0.00 0.00 43.97 1.82
4897 5997 1.478654 GGGCCAAAAGAGTCAGACCAA 60.479 52.381 4.39 0.00 0.00 3.67
5015 6115 7.201785 GGTTGTTCATTAAGGAGAACTTCAACA 60.202 37.037 15.10 2.54 43.38 3.33
5016 6116 7.139392 GGTTGTTCATTAAGGAGAACTTCAAC 58.861 38.462 15.10 11.96 43.38 3.18
5176 6276 3.118261 ACGATTAGTGGGCACATGAAGAT 60.118 43.478 0.00 0.00 0.00 2.40
5278 6378 3.959293 ACAGAGGATGAATGCATGACAA 58.041 40.909 0.00 0.00 34.11 3.18
5356 6456 2.359107 CACGACCAGTGCCTGCAT 60.359 61.111 0.00 0.00 44.72 3.96
5725 6826 3.936203 GTGACACCGGCCCAGACA 61.936 66.667 0.00 0.00 0.00 3.41
6190 7291 2.242965 TCAATGGACCCATCAGAATGCT 59.757 45.455 1.48 0.00 35.31 3.79
6464 7565 4.870636 TCAGACCATAAATTGCCTTGGAT 58.129 39.130 0.00 0.00 33.36 3.41
6829 7930 2.829720 GTGGTAGACATGGGTGTAGTCA 59.170 50.000 0.00 0.00 39.09 3.41
6865 7966 3.953612 AGAAAGAAGCACACCATCAACAA 59.046 39.130 0.00 0.00 0.00 2.83
7309 8410 2.441750 GGAGGCTGTGATTGGGGTATAA 59.558 50.000 0.00 0.00 0.00 0.98
7681 8786 2.649816 ACAATAGGCTTTGAGGGGAACT 59.350 45.455 13.77 0.00 0.00 3.01
8205 9320 1.966451 GGGTCGCCAACAGAACTGG 60.966 63.158 6.76 0.00 36.99 4.00
8300 9415 2.268762 TAGTGCATGTCCAAACTGCA 57.731 45.000 0.00 0.00 43.20 4.41
8344 9459 1.581934 CAGAAACAAGAGTCCGTGCA 58.418 50.000 0.00 0.00 0.00 4.57
8404 9540 2.028748 ACAGCATTTCCAACAGAATGGC 60.029 45.455 0.00 0.00 43.62 4.40
8520 9661 4.700692 AGCCTCATATGAATAGCAGCAATG 59.299 41.667 18.89 0.53 0.00 2.82
8556 9697 4.079385 TCTCAGCTGTTACTACTATCCCCA 60.079 45.833 14.67 0.00 0.00 4.96
8651 9823 7.313646 CACAATCTGAGAGCATCAAAATCTTT 58.686 34.615 0.00 0.00 37.52 2.52
8714 9886 1.202405 GCCCCAATAATTGACTTGCCG 60.202 52.381 0.00 0.00 0.00 5.69
8716 9888 2.739609 GCTGCCCCAATAATTGACTTGC 60.740 50.000 0.00 0.00 0.00 4.01
8749 9921 2.972625 TCGCAATCGAAGAACCAGATT 58.027 42.857 0.00 0.00 43.58 2.40
8771 9943 3.652274 CTTGCAAATGGTGGTTCGAATT 58.348 40.909 0.00 0.00 0.00 2.17
8779 9952 2.188062 AATTGGCTTGCAAATGGTGG 57.812 45.000 0.00 0.00 0.00 4.61
8814 9987 7.161773 TCAAGTTACTATTACCTTAGCACGT 57.838 36.000 0.00 0.00 0.00 4.49
8851 10027 3.448686 CAGGACACACTATTCTTAGGCG 58.551 50.000 0.00 0.00 0.00 5.52
8871 10058 1.808512 CGTATCATAGTTTGGCCGCCA 60.809 52.381 8.43 8.43 0.00 5.69
8905 10092 2.675348 GGCTAGCAGCAAAGAGTAACTG 59.325 50.000 18.24 0.00 44.75 3.16
8906 10093 2.569404 AGGCTAGCAGCAAAGAGTAACT 59.431 45.455 18.24 0.00 44.75 2.24
8907 10094 2.933260 GAGGCTAGCAGCAAAGAGTAAC 59.067 50.000 18.24 0.00 44.75 2.50
8908 10095 2.093447 GGAGGCTAGCAGCAAAGAGTAA 60.093 50.000 18.24 0.00 44.75 2.24
8909 10096 1.482593 GGAGGCTAGCAGCAAAGAGTA 59.517 52.381 18.24 0.00 44.75 2.59
8910 10097 0.251634 GGAGGCTAGCAGCAAAGAGT 59.748 55.000 18.24 0.00 44.75 3.24
8911 10098 0.540923 AGGAGGCTAGCAGCAAAGAG 59.459 55.000 18.24 0.00 44.75 2.85
8912 10099 0.539051 GAGGAGGCTAGCAGCAAAGA 59.461 55.000 18.24 0.00 44.75 2.52
8913 10100 0.463474 GGAGGAGGCTAGCAGCAAAG 60.463 60.000 18.24 0.00 44.75 2.77
8914 10101 1.200760 TGGAGGAGGCTAGCAGCAAA 61.201 55.000 18.24 0.00 44.75 3.68
8915 10102 0.984961 ATGGAGGAGGCTAGCAGCAA 60.985 55.000 18.24 0.00 44.75 3.91
8916 10103 0.984961 AATGGAGGAGGCTAGCAGCA 60.985 55.000 18.24 0.00 44.75 4.41
8917 10104 0.182299 AAATGGAGGAGGCTAGCAGC 59.818 55.000 18.24 7.31 41.46 5.25
8918 10105 4.041444 AGAATAAATGGAGGAGGCTAGCAG 59.959 45.833 18.24 0.00 0.00 4.24
8919 10106 3.976654 AGAATAAATGGAGGAGGCTAGCA 59.023 43.478 18.24 0.00 0.00 3.49
8920 10107 4.632327 AGAATAAATGGAGGAGGCTAGC 57.368 45.455 6.04 6.04 0.00 3.42
8921 10108 7.487822 TCATAGAATAAATGGAGGAGGCTAG 57.512 40.000 0.00 0.00 0.00 3.42
8922 10109 7.903481 AGATCATAGAATAAATGGAGGAGGCTA 59.097 37.037 0.00 0.00 0.00 3.93
8923 10110 6.734755 AGATCATAGAATAAATGGAGGAGGCT 59.265 38.462 0.00 0.00 0.00 4.58
8924 10111 6.956497 AGATCATAGAATAAATGGAGGAGGC 58.044 40.000 0.00 0.00 0.00 4.70
8925 10112 8.824783 AGAAGATCATAGAATAAATGGAGGAGG 58.175 37.037 0.00 0.00 0.00 4.30
8926 10113 9.656040 CAGAAGATCATAGAATAAATGGAGGAG 57.344 37.037 0.00 0.00 0.00 3.69
8927 10114 8.099537 GCAGAAGATCATAGAATAAATGGAGGA 58.900 37.037 0.00 0.00 0.00 3.71
8956 10143 8.349983 GTGGAACAACAACTACTTTATCATTGT 58.650 33.333 0.00 0.00 44.16 2.71
8982 10169 2.082231 CATGAAGAAGCTGTGACCCTG 58.918 52.381 0.00 0.00 0.00 4.45
9013 10206 6.002062 ACCTTATTTTTCGCAACTGAAGAG 57.998 37.500 0.00 0.00 0.00 2.85
9037 10230 1.848608 CTACAGCACGACGACATGATG 59.151 52.381 0.00 0.60 38.20 3.07
9074 10267 5.989777 CCGTCTCTATGGTCGGAAATTATTT 59.010 40.000 0.00 0.00 44.86 1.40
9084 10277 1.202734 TCTACCCCGTCTCTATGGTCG 60.203 57.143 0.00 0.00 32.27 4.79
9088 10281 2.660670 AGGTCTACCCCGTCTCTATG 57.339 55.000 0.00 0.00 36.42 2.23
9111 10304 3.275143 CGTTGTGCCTGGTGGATTAATA 58.725 45.455 0.00 0.00 34.57 0.98


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

AutoCloner maintained by Alex Coulton.