Multiple sequence alignment - TraesCS3A01G230900

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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 TraesCS3A01G230900 chr3A 100.000 4958 0 0 1 4958 431070591 431075548 0.000000e+00 9156.0
1 TraesCS3A01G230900 chr3A 87.568 185 17 2 3349 3533 668638227 668638405 5.030000e-50 209.0
2 TraesCS3A01G230900 chr3A 85.106 188 22 2 3349 3536 718742105 718741924 2.360000e-43 187.0
3 TraesCS3A01G230900 chr3D 95.975 1441 51 3 595 2033 303466567 303465132 0.000000e+00 2333.0
4 TraesCS3A01G230900 chr3D 95.676 925 39 1 3199 4122 303463910 303462986 0.000000e+00 1485.0
5 TraesCS3A01G230900 chr3D 88.411 768 77 7 4193 4958 303433750 303432993 0.000000e+00 915.0
6 TraesCS3A01G230900 chr3D 86.957 115 10 4 4114 4223 81696999 81696885 1.870000e-24 124.0
7 TraesCS3A01G230900 chr3D 100.000 56 0 0 2003 2058 303465130 303465075 2.440000e-18 104.0
8 TraesCS3A01G230900 chr3D 88.710 62 6 1 3140 3201 384418876 384418936 1.910000e-09 75.0
9 TraesCS3A01G230900 chr3B 94.331 1376 45 13 697 2072 417957119 417958461 0.000000e+00 2078.0
10 TraesCS3A01G230900 chr3B 94.415 949 44 3 3202 4143 417958560 417959506 0.000000e+00 1450.0
11 TraesCS3A01G230900 chr3B 88.424 812 79 10 4153 4958 417960307 417961109 0.000000e+00 965.0
12 TraesCS3A01G230900 chr3B 87.967 482 36 11 2737 3199 820860773 820861251 2.610000e-152 549.0
13 TraesCS3A01G230900 chr3B 78.627 641 128 7 4321 4958 733081455 733082089 2.760000e-112 416.0
14 TraesCS3A01G230900 chr3B 84.314 408 46 14 13 407 741347739 741347337 2.800000e-102 383.0
15 TraesCS3A01G230900 chr3B 84.770 348 15 12 2092 2410 820732260 820732598 1.040000e-81 315.0
16 TraesCS3A01G230900 chr3B 76.817 578 120 12 4373 4944 242104105 242104674 3.730000e-81 313.0
17 TraesCS3A01G230900 chr3B 80.851 282 50 4 4507 4787 43564530 43564808 8.360000e-53 219.0
18 TraesCS3A01G230900 chr3B 75.870 431 99 5 4365 4792 412701640 412701212 1.080000e-51 215.0
19 TraesCS3A01G230900 chr3B 87.006 177 16 3 2441 2613 820800095 820800268 5.060000e-45 193.0
20 TraesCS3A01G230900 chr3B 88.288 111 9 3 4116 4222 31124879 31124989 4.030000e-26 130.0
21 TraesCS3A01G230900 chr4A 92.269 983 59 11 2092 3063 639019515 639018539 0.000000e+00 1378.0
22 TraesCS3A01G230900 chr4A 78.993 576 119 2 4352 4926 54640363 54639789 4.650000e-105 392.0
23 TraesCS3A01G230900 chr4A 91.228 57 5 0 3145 3201 666251932 666251988 1.480000e-10 78.7
24 TraesCS3A01G230900 chr5A 88.769 1113 90 19 2094 3193 424904487 424905577 0.000000e+00 1330.0
25 TraesCS3A01G230900 chr5A 96.820 283 9 0 7 289 581492887 581492605 1.620000e-129 473.0
26 TraesCS3A01G230900 chr5A 88.561 271 31 0 288 558 372645068 372645338 3.700000e-86 329.0
27 TraesCS3A01G230900 chr2B 98.233 283 5 0 8 290 675210661 675210943 3.450000e-136 496.0
28 TraesCS3A01G230900 chr2B 76.630 184 43 0 1613 1796 252977104 252976921 8.780000e-18 102.0
29 TraesCS3A01G230900 chr2B 85.135 74 6 5 3135 3205 621186990 621187061 2.480000e-08 71.3
30 TraesCS3A01G230900 chr1A 82.931 539 80 8 13 543 564269253 564268719 4.490000e-130 475.0
31 TraesCS3A01G230900 chr1A 91.475 305 20 3 13 315 14434694 14434394 9.930000e-112 414.0
32 TraesCS3A01G230900 chr1A 85.405 185 21 2 3349 3533 343963378 343963556 2.360000e-43 187.0
33 TraesCS3A01G230900 chr1A 77.236 246 49 5 4370 4612 11161627 11161386 2.410000e-28 137.0
34 TraesCS3A01G230900 chr1A 75.697 251 51 8 4352 4596 354830124 354829878 3.140000e-22 117.0
35 TraesCS3A01G230900 chr1A 85.333 75 7 4 3130 3201 57736251 57736178 1.910000e-09 75.0
36 TraesCS3A01G230900 chrUn 96.809 282 9 0 11 292 312185510 312185229 5.810000e-129 472.0
37 TraesCS3A01G230900 chrUn 87.611 113 10 3 4114 4222 29812785 29812897 1.450000e-25 128.0
38 TraesCS3A01G230900 chrUn 84.252 127 14 5 4100 4222 171907509 171907633 8.720000e-23 119.0
39 TraesCS3A01G230900 chrUn 84.252 127 14 5 4100 4222 287879366 287879490 8.720000e-23 119.0
40 TraesCS3A01G230900 chrUn 84.252 127 14 5 4100 4222 383415901 383416025 8.720000e-23 119.0
41 TraesCS3A01G230900 chr4B 97.133 279 8 0 11 289 117068283 117068561 5.810000e-129 472.0
42 TraesCS3A01G230900 chr4B 97.133 279 8 0 11 289 117089375 117089653 5.810000e-129 472.0
43 TraesCS3A01G230900 chr4B 91.071 56 5 0 3146 3201 349156098 349156043 5.320000e-10 76.8
44 TraesCS3A01G230900 chr4B 87.273 55 7 0 1728 1782 672308679 672308625 4.140000e-06 63.9
45 TraesCS3A01G230900 chr1D 82.353 544 68 20 13 540 420837763 420838294 9.790000e-122 448.0
46 TraesCS3A01G230900 chr6A 83.784 444 62 6 11 447 455984596 455984156 3.570000e-111 412.0
47 TraesCS3A01G230900 chr6A 91.882 271 22 0 288 558 410761977 410761707 3.620000e-101 379.0
48 TraesCS3A01G230900 chr6A 89.091 275 30 0 288 562 92053524 92053250 4.750000e-90 342.0
49 TraesCS3A01G230900 chr6A 88.043 276 31 2 288 562 470142514 470142240 4.790000e-85 326.0
50 TraesCS3A01G230900 chr6A 90.000 110 10 1 4114 4222 529027274 529027383 1.860000e-29 141.0
51 TraesCS3A01G230900 chr1B 89.524 315 26 3 13 320 612399941 612400255 4.650000e-105 392.0
52 TraesCS3A01G230900 chr1B 78.551 345 70 3 4455 4797 662152563 662152221 1.800000e-54 224.0
53 TraesCS3A01G230900 chr7A 89.677 310 24 5 13 315 604404343 604404035 6.020000e-104 388.0
54 TraesCS3A01G230900 chr7A 89.062 64 4 3 3139 3201 90031855 90031794 5.320000e-10 76.8
55 TraesCS3A01G230900 chr7B 79.374 543 88 19 13 545 678088651 678089179 1.310000e-95 361.0
56 TraesCS3A01G230900 chr2A 89.377 273 26 1 288 560 21918542 21918273 1.710000e-89 340.0
57 TraesCS3A01G230900 chr2A 84.865 185 22 2 3349 3533 469876390 469876568 1.100000e-41 182.0
58 TraesCS3A01G230900 chr2A 76.364 275 59 6 1613 1884 211695009 211694738 5.170000e-30 143.0
59 TraesCS3A01G230900 chr6B 78.082 511 93 16 11 509 50406113 50406616 6.240000e-79 305.0
60 TraesCS3A01G230900 chr5D 79.718 355 69 2 4585 4939 2134441 2134792 2.290000e-63 254.0
61 TraesCS3A01G230900 chr5D 76.168 214 51 0 1605 1818 510058795 510059008 4.060000e-21 113.0
62 TraesCS3A01G230900 chr5B 76.596 282 62 4 3416 3695 641043561 641043840 8.600000e-33 152.0
63 TraesCS3A01G230900 chr5B 85.714 126 11 6 4102 4222 271021149 271021272 5.210000e-25 126.0
64 TraesCS3A01G230900 chr5B 80.556 144 27 1 4809 4952 670389007 670388865 5.250000e-20 110.0
65 TraesCS3A01G230900 chr5B 75.701 214 52 0 1605 1818 641043190 641043403 1.890000e-19 108.0
66 TraesCS3A01G230900 chr2D 77.725 211 45 2 1613 1822 196130844 196130635 1.450000e-25 128.0
67 TraesCS3A01G230900 chr2D 83.333 102 17 0 1695 1796 196224306 196224205 1.470000e-15 95.3
68 TraesCS3A01G230900 chr7D 88.060 67 3 4 3139 3203 623706596 623706659 1.910000e-09 75.0
69 TraesCS3A01G230900 chr7D 84.615 78 6 5 3139 3212 578070431 578070356 6.880000e-09 73.1


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 TraesCS3A01G230900 chr3A 431070591 431075548 4957 False 9156.000000 9156 100.000 1 4958 1 chr3A.!!$F1 4957
1 TraesCS3A01G230900 chr3D 303462986 303466567 3581 True 1307.333333 2333 97.217 595 4122 3 chr3D.!!$R3 3527
2 TraesCS3A01G230900 chr3D 303432993 303433750 757 True 915.000000 915 88.411 4193 4958 1 chr3D.!!$R2 765
3 TraesCS3A01G230900 chr3B 417957119 417961109 3990 False 1497.666667 2078 92.390 697 4958 3 chr3B.!!$F8 4261
4 TraesCS3A01G230900 chr3B 733081455 733082089 634 False 416.000000 416 78.627 4321 4958 1 chr3B.!!$F4 637
5 TraesCS3A01G230900 chr3B 242104105 242104674 569 False 313.000000 313 76.817 4373 4944 1 chr3B.!!$F3 571
6 TraesCS3A01G230900 chr4A 639018539 639019515 976 True 1378.000000 1378 92.269 2092 3063 1 chr4A.!!$R2 971
7 TraesCS3A01G230900 chr4A 54639789 54640363 574 True 392.000000 392 78.993 4352 4926 1 chr4A.!!$R1 574
8 TraesCS3A01G230900 chr5A 424904487 424905577 1090 False 1330.000000 1330 88.769 2094 3193 1 chr5A.!!$F2 1099
9 TraesCS3A01G230900 chr1A 564268719 564269253 534 True 475.000000 475 82.931 13 543 1 chr1A.!!$R5 530
10 TraesCS3A01G230900 chr1D 420837763 420838294 531 False 448.000000 448 82.353 13 540 1 chr1D.!!$F1 527
11 TraesCS3A01G230900 chr7B 678088651 678089179 528 False 361.000000 361 79.374 13 545 1 chr7B.!!$F1 532
12 TraesCS3A01G230900 chr6B 50406113 50406616 503 False 305.000000 305 78.082 11 509 1 chr6B.!!$F1 498

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
579 585 0.313987 TGTCACGTCTCGATGTGCTT 59.686 50.000 13.12 0.00 45.44 3.91 F
636 642 0.370273 CTTGGAAGTCGTATGTGCGC 59.630 55.000 0.00 0.00 0.00 6.09 F
1017 1023 1.532316 CATGGCCATGACATCCCCC 60.532 63.158 37.84 0.00 41.20 5.40 F
2315 3434 0.816421 AAAGTAACACCGCGCCAGTT 60.816 50.000 0.00 7.46 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 3298 0.741915 GGGAGAGAAAGATCGAGCGT 59.258 55.000 0.00 0.0 0.00 5.07 R
2315 3434 2.175202 GAGCAGAACTTCTGGGAGAGA 58.825 52.381 18.53 0.0 44.43 3.10 R
2880 4005 0.319083 AATGTTGCTGCATGGTGGTG 59.681 50.000 1.84 0.0 0.00 4.17 R
4223 6149 0.120377 AGGGGAGGTTCCACATACCA 59.880 55.000 0.00 0.0 44.30 3.25 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
158 159 2.159382 GACTCATTTTGCCTCGGGAAA 58.841 47.619 0.00 0.00 33.75 3.13
203 204 3.626930 TGTTACCACAAGCACCTCTTTT 58.373 40.909 0.00 0.00 31.27 2.27
219 220 8.730680 GCACCTCTTTTCTCATTAAATACTTGA 58.269 33.333 0.00 0.00 0.00 3.02
274 275 9.774071 TTAAGTTACTACCTAAGTTACTCCCAT 57.226 33.333 0.00 0.00 45.09 4.00
309 315 7.015389 GCCTTAGTCATAGTGGGAGTAACTTAT 59.985 40.741 0.00 0.00 0.00 1.73
380 386 7.009179 AGTTAATGAGGAGAGATGTGTTTGA 57.991 36.000 0.00 0.00 0.00 2.69
390 396 8.543774 AGGAGAGATGTGTTTGAAGTAACATAT 58.456 33.333 0.00 0.00 40.92 1.78
419 425 4.794169 ACCATCACATAACGCTTTTCAAC 58.206 39.130 0.00 0.00 0.00 3.18
424 430 6.746104 TCACATAACGCTTTTCAACAAATG 57.254 33.333 0.00 0.00 0.00 2.32
425 431 6.269315 TCACATAACGCTTTTCAACAAATGT 58.731 32.000 0.00 0.00 0.00 2.71
452 458 8.424133 TGAGTCTATGAGCAAATAAATAGAGCA 58.576 33.333 0.00 0.00 33.45 4.26
454 460 9.050601 AGTCTATGAGCAAATAAATAGAGCAAC 57.949 33.333 0.00 0.00 33.45 4.17
522 528 8.470657 AACTTAGACTAGTCTCATATGCATGA 57.529 34.615 28.42 4.61 40.93 3.07
545 551 8.474710 TGATATTAGTCTAAGTTACTCCCCAC 57.525 38.462 0.00 0.00 0.00 4.61
546 552 8.287350 TGATATTAGTCTAAGTTACTCCCCACT 58.713 37.037 0.00 0.00 0.00 4.00
547 553 9.804977 GATATTAGTCTAAGTTACTCCCCACTA 57.195 37.037 0.00 0.00 0.00 2.74
551 557 7.894753 AGTCTAAGTTACTCCCCACTATAAC 57.105 40.000 0.00 0.00 0.00 1.89
552 558 6.838090 AGTCTAAGTTACTCCCCACTATAACC 59.162 42.308 0.00 0.00 0.00 2.85
553 559 6.608808 GTCTAAGTTACTCCCCACTATAACCA 59.391 42.308 0.00 0.00 0.00 3.67
554 560 5.952347 AAGTTACTCCCCACTATAACCAG 57.048 43.478 0.00 0.00 0.00 4.00
555 561 3.710165 AGTTACTCCCCACTATAACCAGC 59.290 47.826 0.00 0.00 0.00 4.85
556 562 1.508256 ACTCCCCACTATAACCAGCC 58.492 55.000 0.00 0.00 0.00 4.85
557 563 1.009675 ACTCCCCACTATAACCAGCCT 59.990 52.381 0.00 0.00 0.00 4.58
558 564 2.127708 CTCCCCACTATAACCAGCCTT 58.872 52.381 0.00 0.00 0.00 4.35
559 565 3.311103 ACTCCCCACTATAACCAGCCTTA 60.311 47.826 0.00 0.00 0.00 2.69
560 566 3.910627 CTCCCCACTATAACCAGCCTTAT 59.089 47.826 0.00 0.00 0.00 1.73
561 567 3.650942 TCCCCACTATAACCAGCCTTATG 59.349 47.826 0.00 0.00 0.00 1.90
562 568 3.394606 CCCCACTATAACCAGCCTTATGT 59.605 47.826 0.00 0.00 0.00 2.29
563 569 4.505039 CCCCACTATAACCAGCCTTATGTC 60.505 50.000 0.00 0.00 0.00 3.06
564 570 4.102524 CCCACTATAACCAGCCTTATGTCA 59.897 45.833 0.00 0.00 0.00 3.58
565 571 5.057149 CCACTATAACCAGCCTTATGTCAC 58.943 45.833 0.00 0.00 0.00 3.67
566 572 4.745125 CACTATAACCAGCCTTATGTCACG 59.255 45.833 0.00 0.00 0.00 4.35
567 573 3.906720 ATAACCAGCCTTATGTCACGT 57.093 42.857 0.00 0.00 0.00 4.49
568 574 2.094762 AACCAGCCTTATGTCACGTC 57.905 50.000 0.00 0.00 0.00 4.34
569 575 1.267121 ACCAGCCTTATGTCACGTCT 58.733 50.000 0.00 0.00 0.00 4.18
570 576 1.204941 ACCAGCCTTATGTCACGTCTC 59.795 52.381 0.00 0.00 0.00 3.36
571 577 1.550065 CAGCCTTATGTCACGTCTCG 58.450 55.000 0.00 0.00 0.00 4.04
572 578 1.132453 CAGCCTTATGTCACGTCTCGA 59.868 52.381 0.00 0.00 0.00 4.04
573 579 2.025155 AGCCTTATGTCACGTCTCGAT 58.975 47.619 0.00 0.00 0.00 3.59
574 580 2.120232 GCCTTATGTCACGTCTCGATG 58.880 52.381 0.00 0.00 0.00 3.84
575 581 2.479730 GCCTTATGTCACGTCTCGATGT 60.480 50.000 0.00 0.00 0.00 3.06
576 582 3.108881 CCTTATGTCACGTCTCGATGTG 58.891 50.000 11.99 11.99 46.78 3.21
577 583 2.188837 TATGTCACGTCTCGATGTGC 57.811 50.000 13.12 9.53 45.44 4.57
578 584 0.528017 ATGTCACGTCTCGATGTGCT 59.472 50.000 13.12 0.30 45.44 4.40
579 585 0.313987 TGTCACGTCTCGATGTGCTT 59.686 50.000 13.12 0.00 45.44 3.91
580 586 1.269569 TGTCACGTCTCGATGTGCTTT 60.270 47.619 13.12 0.00 45.44 3.51
581 587 2.030628 TGTCACGTCTCGATGTGCTTTA 60.031 45.455 13.12 0.00 45.44 1.85
582 588 2.594654 GTCACGTCTCGATGTGCTTTAG 59.405 50.000 13.12 0.00 45.44 1.85
583 589 1.321743 CACGTCTCGATGTGCTTTAGC 59.678 52.381 6.35 0.00 40.88 3.09
584 590 0.567968 CGTCTCGATGTGCTTTAGCG 59.432 55.000 0.00 0.00 45.83 4.26
585 591 1.794076 CGTCTCGATGTGCTTTAGCGA 60.794 52.381 0.00 0.00 45.83 4.93
586 592 2.259618 GTCTCGATGTGCTTTAGCGAA 58.740 47.619 0.00 0.00 45.83 4.70
587 593 2.666508 GTCTCGATGTGCTTTAGCGAAA 59.333 45.455 0.00 0.00 45.83 3.46
588 594 3.122948 GTCTCGATGTGCTTTAGCGAAAA 59.877 43.478 0.00 0.00 45.83 2.29
589 595 3.122948 TCTCGATGTGCTTTAGCGAAAAC 59.877 43.478 0.00 0.00 45.83 2.43
590 596 3.064207 TCGATGTGCTTTAGCGAAAACT 58.936 40.909 0.00 0.00 45.83 2.66
591 597 3.120683 TCGATGTGCTTTAGCGAAAACTG 60.121 43.478 0.00 0.00 45.83 3.16
592 598 3.363970 CGATGTGCTTTAGCGAAAACTGT 60.364 43.478 0.00 0.00 45.83 3.55
593 599 4.537015 GATGTGCTTTAGCGAAAACTGTT 58.463 39.130 0.00 0.00 45.83 3.16
617 623 1.217882 AATGCGCTAACATAGTCGCC 58.782 50.000 9.73 6.37 44.61 5.54
622 628 1.202371 CGCTAACATAGTCGCCTTGGA 60.202 52.381 0.00 0.00 0.00 3.53
629 635 1.825090 TAGTCGCCTTGGAAGTCGTA 58.175 50.000 0.00 0.00 0.00 3.43
636 642 0.370273 CTTGGAAGTCGTATGTGCGC 59.630 55.000 0.00 0.00 0.00 6.09
667 673 2.081526 CGAGGACGTGCTCAATTGG 58.918 57.895 32.29 14.99 34.56 3.16
748 754 4.904154 CGATTGAAGTTTCGAAGAAACCAC 59.096 41.667 18.51 14.02 45.90 4.16
761 767 5.404667 CGAAGAAACCACTCACTAGGTTAAC 59.595 44.000 0.00 0.00 46.92 2.01
773 779 1.816679 GGTTAACGGGTCGCATCCC 60.817 63.158 0.00 3.35 43.78 3.85
858 864 2.346766 TGGTCAATCATCAATCCCCG 57.653 50.000 0.00 0.00 0.00 5.73
861 867 2.358898 GGTCAATCATCAATCCCCGTTG 59.641 50.000 0.00 0.00 0.00 4.10
902 908 4.443913 TTTTACGGCTCCAATTAAAGGC 57.556 40.909 3.47 3.47 34.90 4.35
954 960 4.582701 AGCACCTGATTAGAAGATCGAG 57.417 45.455 0.00 0.00 0.00 4.04
985 991 2.347490 CCCCACTGCTACAGCGTT 59.653 61.111 0.00 0.00 45.83 4.84
1017 1023 1.532316 CATGGCCATGACATCCCCC 60.532 63.158 37.84 0.00 41.20 5.40
1332 1338 4.803426 CACGTCCTGCTCGCCCTC 62.803 72.222 0.00 0.00 0.00 4.30
1912 1918 1.643832 GAAGATGTCGATTGCGCCC 59.356 57.895 4.18 0.00 37.46 6.13
2060 2100 6.565999 CGAACAAACTGCTTTAGTCCTTTAGG 60.566 42.308 0.00 0.00 39.18 2.69
2072 3176 8.619683 TTTAGTCCTTTAGGCTATTCTTACCT 57.380 34.615 0.00 0.00 37.61 3.08
2073 3177 6.487299 AGTCCTTTAGGCTATTCTTACCTG 57.513 41.667 0.00 0.00 34.92 4.00
2074 3178 6.203072 AGTCCTTTAGGCTATTCTTACCTGA 58.797 40.000 0.00 0.00 34.92 3.86
2075 3179 6.098552 AGTCCTTTAGGCTATTCTTACCTGAC 59.901 42.308 0.00 0.00 34.92 3.51
2076 3180 5.365895 TCCTTTAGGCTATTCTTACCTGACC 59.634 44.000 0.00 0.00 34.92 4.02
2089 3193 7.786046 TCTTACCTGACCAGTACTATTTTCA 57.214 36.000 0.00 0.00 0.00 2.69
2213 3327 3.790089 TCTTTCTCTCCCCAGTTTTCC 57.210 47.619 0.00 0.00 0.00 3.13
2279 3393 4.463186 GCTACTCCTTACTCTCCAAGAACA 59.537 45.833 0.00 0.00 0.00 3.18
2315 3434 0.816421 AAAGTAACACCGCGCCAGTT 60.816 50.000 0.00 7.46 0.00 3.16
2345 3464 1.786937 AGTTCTGCTCGATGGATCCT 58.213 50.000 14.23 0.00 0.00 3.24
2361 3480 6.764308 TGGATCCTGAACAAAATCAATCTC 57.236 37.500 14.23 0.00 0.00 2.75
2409 3528 9.162764 TGTTCTTTCTTTACCTAGCATGTATTC 57.837 33.333 0.00 0.00 0.00 1.75
2422 3541 9.167311 CCTAGCATGTATTCTTTTGACTACTTT 57.833 33.333 0.00 0.00 36.10 2.66
2474 3595 8.943594 AAAACCTTTGTTCCCATGTACTAATA 57.056 30.769 0.00 0.00 32.15 0.98
2475 3596 8.943594 AAACCTTTGTTCCCATGTACTAATAA 57.056 30.769 0.00 0.00 32.15 1.40
2476 3597 9.541884 AAACCTTTGTTCCCATGTACTAATAAT 57.458 29.630 0.00 0.00 32.15 1.28
2477 3598 8.519799 ACCTTTGTTCCCATGTACTAATAATG 57.480 34.615 0.00 0.00 0.00 1.90
2511 3632 1.678728 GCACCATCCGGATTCACAGAA 60.679 52.381 16.19 0.00 35.59 3.02
2519 3640 6.488006 CCATCCGGATTCACAGAATATTTTCT 59.512 38.462 16.19 0.00 43.09 2.52
2554 3675 5.623368 CGTGTTGTATACCCATTGGCAATTT 60.623 40.000 10.65 0.41 33.59 1.82
2556 3677 6.091986 GTGTTGTATACCCATTGGCAATTTTG 59.908 38.462 10.65 0.62 33.59 2.44
2557 3678 5.350504 TGTATACCCATTGGCAATTTTGG 57.649 39.130 10.65 10.69 33.59 3.28
2595 3718 7.512992 AGACTCCTGGACATAAAATGATAAGG 58.487 38.462 0.00 0.00 0.00 2.69
2609 3732 7.707624 AAATGATAAGGTTTCTTGATCTGCA 57.292 32.000 0.00 0.00 34.59 4.41
2671 3794 5.818136 ATCGTGGTCCAAGATACAAATTG 57.182 39.130 17.62 0.00 31.44 2.32
2750 3873 6.371825 CGCCTAAACCTTGAGTTCTAAATCTT 59.628 38.462 0.00 0.00 37.88 2.40
2825 3950 5.516339 GTGAACCAATTTACATATGTGCAGC 59.484 40.000 18.81 0.00 0.00 5.25
2839 3964 4.944962 TGTGCAGCACTAATGTTCATAC 57.055 40.909 25.83 0.00 35.11 2.39
2862 3987 3.684305 TGTTAAGCAATCGTCCATGTCTG 59.316 43.478 0.00 0.00 0.00 3.51
2879 4004 6.347969 CCATGTCTGAACTATTTGTCACACAG 60.348 42.308 0.00 0.00 0.00 3.66
2880 4005 4.511454 TGTCTGAACTATTTGTCACACAGC 59.489 41.667 0.00 0.00 0.00 4.40
2913 4038 2.161855 CAACATTGCCTTCCTAGCACA 58.838 47.619 0.00 0.00 40.69 4.57
2925 4050 1.347707 CCTAGCACAGTTCACCCTTGA 59.652 52.381 0.00 0.00 0.00 3.02
2975 4100 1.337728 TGGTGTCACTACCGCTTGATG 60.338 52.381 2.35 0.00 43.87 3.07
2989 4114 2.940971 GCTTGATGTCATGTGCACCCTA 60.941 50.000 15.69 0.00 0.00 3.53
2991 4116 2.187100 TGATGTCATGTGCACCCTAGA 58.813 47.619 15.69 3.92 0.00 2.43
3068 4194 4.678309 GCGCAAACTAGAGAAGGTATGTCT 60.678 45.833 0.30 0.00 35.49 3.41
3070 4196 5.353111 GCAAACTAGAGAAGGTATGTCTCC 58.647 45.833 0.00 0.00 42.17 3.71
3076 4202 5.269505 AGAGAAGGTATGTCTCCAATTCG 57.730 43.478 0.00 0.00 42.17 3.34
3085 4211 7.834681 AGGTATGTCTCCAATTCGCTATCTATA 59.165 37.037 0.00 0.00 0.00 1.31
3106 4232 0.252057 AAAACCCTATGCCACACCCC 60.252 55.000 0.00 0.00 0.00 4.95
3124 4250 2.749600 CCCCCATGTGATTTTCCATGA 58.250 47.619 0.00 0.00 40.70 3.07
3128 4254 4.937015 CCCCATGTGATTTTCCATGAAAAC 59.063 41.667 4.28 1.09 42.98 2.43
3130 4256 5.640357 CCCATGTGATTTTCCATGAAAACTG 59.360 40.000 4.28 0.00 42.98 3.16
3131 4257 6.457355 CCATGTGATTTTCCATGAAAACTGA 58.543 36.000 4.28 0.00 42.98 3.41
3132 4258 7.101054 CCATGTGATTTTCCATGAAAACTGAT 58.899 34.615 4.28 0.00 42.98 2.90
3151 4277 9.884636 AAACTGATAACCAATATTAAAAAGGCC 57.115 29.630 0.00 0.00 0.00 5.19
3154 4280 6.903534 TGATAACCAATATTAAAAAGGCCCCA 59.096 34.615 0.00 0.00 0.00 4.96
3193 4319 1.527370 CCCCCGAAATCTCAGGACC 59.473 63.158 0.00 0.00 0.00 4.46
3194 4320 1.144057 CCCCGAAATCTCAGGACCG 59.856 63.158 0.00 0.00 0.00 4.79
3195 4321 1.144057 CCCGAAATCTCAGGACCGG 59.856 63.158 0.00 0.00 34.41 5.28
3196 4322 1.521681 CCGAAATCTCAGGACCGGC 60.522 63.158 0.00 0.00 0.00 6.13
3197 4323 1.521681 CGAAATCTCAGGACCGGCC 60.522 63.158 0.00 3.58 0.00 6.13
3198 4324 1.153147 GAAATCTCAGGACCGGCCC 60.153 63.158 0.00 0.00 37.37 5.80
3199 4325 1.616628 AAATCTCAGGACCGGCCCT 60.617 57.895 2.07 2.07 37.37 5.19
3214 4340 2.187946 CCTGATCGCACCCTCACC 59.812 66.667 0.00 0.00 0.00 4.02
3215 4341 2.659063 CCTGATCGCACCCTCACCA 61.659 63.158 0.00 0.00 0.00 4.17
3241 4367 3.805422 ACGAAAACGACAGCACTGATTTA 59.195 39.130 4.31 0.00 0.00 1.40
3302 4428 8.195436 GTCACTGTATAGGCAACAACTCTATAA 58.805 37.037 0.00 0.00 41.41 0.98
3319 4445 1.917273 TAATCGTTGCCGTGCTACTC 58.083 50.000 8.28 0.00 32.61 2.59
3346 4472 1.165907 TCCAACAAGAGCAGTTGCCG 61.166 55.000 0.00 0.00 43.74 5.69
3373 4499 1.904287 TCCTGTGGTTTCCAAATCGG 58.096 50.000 0.00 0.00 34.18 4.18
3429 4555 0.668706 CTTGCCAGGTCACTCTGTCG 60.669 60.000 0.00 0.00 33.14 4.35
3456 4582 1.603455 CAACATGGTGGACGGCCTT 60.603 57.895 9.82 0.00 34.31 4.35
3511 4637 0.395036 CACCACCAACCACAAGGACA 60.395 55.000 0.00 0.00 38.69 4.02
3635 4761 0.325296 ATCCAAGACCACCCGCTCTA 60.325 55.000 0.00 0.00 0.00 2.43
3639 4765 3.468140 GACCACCCGCTCTACCCC 61.468 72.222 0.00 0.00 0.00 4.95
3643 4769 4.835891 ACCCGCTCTACCCCGAGG 62.836 72.222 0.00 0.00 40.04 4.63
3727 4853 3.841379 GACGATGCCGATGCCGCTA 62.841 63.158 0.00 0.00 39.50 4.26
3876 5002 0.107081 TTGACGACGGAATTGGTGGT 59.893 50.000 0.00 0.00 0.00 4.16
3988 5114 1.211703 TCCCTCTGTTCAAGTGCACAA 59.788 47.619 21.04 1.11 0.00 3.33
4003 5129 6.327279 AGTGCACAAGGGTCTAAATAAAAC 57.673 37.500 21.04 0.00 0.00 2.43
4006 5132 6.861572 GTGCACAAGGGTCTAAATAAAACTTC 59.138 38.462 13.17 0.00 0.00 3.01
4080 5213 2.351455 TCGCGACCATTAATTTGAGCA 58.649 42.857 3.71 0.00 0.00 4.26
4087 5220 6.972328 GCGACCATTAATTTGAGCAGAATTTA 59.028 34.615 0.00 0.00 0.00 1.40
4118 5251 8.581578 AGTTTTATTAAAATGTTCATGGTCGGT 58.418 29.630 4.97 0.00 32.22 4.69
4130 5263 1.241990 TGGTCGGTTCAGTCTCTCGG 61.242 60.000 0.00 0.00 0.00 4.63
4143 5276 1.490910 TCTCTCGGAGGTGCTCATAGA 59.509 52.381 4.96 0.00 31.08 1.98
4144 5277 1.879380 CTCTCGGAGGTGCTCATAGAG 59.121 57.143 4.96 0.00 35.86 2.43
4145 5278 1.490910 TCTCGGAGGTGCTCATAGAGA 59.509 52.381 4.96 4.64 36.00 3.10
4148 5281 4.075682 CTCGGAGGTGCTCATAGAGATAA 58.924 47.826 0.00 0.00 33.38 1.75
4150 5283 3.192422 CGGAGGTGCTCATAGAGATAAGG 59.808 52.174 0.00 0.00 31.08 2.69
4158 6082 5.046529 GCTCATAGAGATAAGGTGTGTGTG 58.953 45.833 0.00 0.00 0.00 3.82
4160 6084 4.466015 TCATAGAGATAAGGTGTGTGTGCA 59.534 41.667 0.00 0.00 0.00 4.57
4162 6086 4.292186 AGAGATAAGGTGTGTGTGCATT 57.708 40.909 0.00 0.00 0.00 3.56
4170 6094 3.081061 GGTGTGTGTGCATTCATAAGGA 58.919 45.455 0.00 0.00 0.00 3.36
4172 6096 4.439153 GGTGTGTGTGCATTCATAAGGATG 60.439 45.833 0.00 0.00 0.00 3.51
4181 6105 6.707608 GTGCATTCATAAGGATGAGTGTATGA 59.292 38.462 10.81 0.00 46.40 2.15
4182 6106 7.389884 GTGCATTCATAAGGATGAGTGTATGAT 59.610 37.037 10.81 0.00 46.40 2.45
4249 6176 3.197983 TGTGGAACCTCCCCTCATAAAT 58.802 45.455 0.00 0.00 35.03 1.40
4253 6180 6.192044 GTGGAACCTCCCCTCATAAATAAAA 58.808 40.000 0.00 0.00 35.03 1.52
4254 6181 6.666113 GTGGAACCTCCCCTCATAAATAAAAA 59.334 38.462 0.00 0.00 35.03 1.94
4264 6191 7.415229 CCCTCATAAATAAAAAGAAGGTACGC 58.585 38.462 0.00 0.00 0.00 4.42
4279 6206 3.118519 AGGTACGCGGAACCATAAAGATT 60.119 43.478 27.90 8.07 39.64 2.40
4285 6212 3.632145 GCGGAACCATAAAGATTGTCCAT 59.368 43.478 0.00 0.00 0.00 3.41
4325 6252 1.375523 GACCCAAGGCGTACACCTG 60.376 63.158 2.46 0.00 39.93 4.00
4329 6256 4.029809 AAGGCGTACACCTGGGGC 62.030 66.667 2.46 0.00 39.93 5.80
4477 6413 4.960938 TGTTAGAGTTTGTGTCATGCTCT 58.039 39.130 0.00 0.00 39.52 4.09
4482 6418 3.755378 GAGTTTGTGTCATGCTCTGGAAT 59.245 43.478 0.00 0.00 0.00 3.01
4493 6432 0.596083 CTCTGGAATACGAGGCAGCG 60.596 60.000 0.00 0.00 37.29 5.18
4494 6433 1.035385 TCTGGAATACGAGGCAGCGA 61.035 55.000 6.78 0.00 34.83 4.93
4495 6434 0.032678 CTGGAATACGAGGCAGCGAT 59.967 55.000 6.78 0.00 34.83 4.58
4498 6437 1.337260 GGAATACGAGGCAGCGATGAT 60.337 52.381 4.02 0.00 34.83 2.45
4558 6500 1.066071 GTCCCAGTGGAGTTTCTAGCC 60.066 57.143 11.95 0.00 42.85 3.93
4690 6632 2.489722 GTTTGCAGGTTGGATCCTTCTC 59.510 50.000 14.23 0.13 35.37 2.87
4733 6675 1.742831 GACAGTTGTTGTTCTGGTGCA 59.257 47.619 0.00 0.00 41.05 4.57
4744 6687 3.580895 TGTTCTGGTGCACTGGTTCTATA 59.419 43.478 17.98 0.00 0.00 1.31
4788 6731 4.941263 TCCCACTGTCTATTACAACAATGC 59.059 41.667 0.00 0.00 37.74 3.56
4801 6744 1.317613 ACAATGCTTGCTCGGTTTCA 58.682 45.000 0.00 0.00 0.00 2.69
4887 6830 3.821033 AGGTGTTCTACAAACCTGAATGC 59.179 43.478 0.00 0.00 42.78 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.844917 ACTATGACCAGCCTAACCTAAGTATT 59.155 38.462 0.00 0.00 0.00 1.89
1 2 6.267928 CACTATGACCAGCCTAACCTAAGTAT 59.732 42.308 0.00 0.00 0.00 2.12
2 3 5.597182 CACTATGACCAGCCTAACCTAAGTA 59.403 44.000 0.00 0.00 0.00 2.24
3 4 4.406003 CACTATGACCAGCCTAACCTAAGT 59.594 45.833 0.00 0.00 0.00 2.24
4 5 4.202264 CCACTATGACCAGCCTAACCTAAG 60.202 50.000 0.00 0.00 0.00 2.18
5 6 3.709653 CCACTATGACCAGCCTAACCTAA 59.290 47.826 0.00 0.00 0.00 2.69
6 7 3.305720 CCACTATGACCAGCCTAACCTA 58.694 50.000 0.00 0.00 0.00 3.08
7 8 2.119495 CCACTATGACCAGCCTAACCT 58.881 52.381 0.00 0.00 0.00 3.50
8 9 1.141053 CCCACTATGACCAGCCTAACC 59.859 57.143 0.00 0.00 0.00 2.85
9 10 1.141053 CCCCACTATGACCAGCCTAAC 59.859 57.143 0.00 0.00 0.00 2.34
131 132 4.442052 CCGAGGCAAAATGAGTCTATGAGA 60.442 45.833 0.00 0.00 0.00 3.27
203 204 9.665719 TGCTTATGTGTCAAGTATTTAATGAGA 57.334 29.630 0.00 0.00 0.00 3.27
219 220 5.304101 TCCCAAGACAATTTTGCTTATGTGT 59.696 36.000 0.00 0.00 0.00 3.72
274 275 5.246203 CCACTATGACTAAGGCTAGCCATAA 59.754 44.000 34.70 18.23 32.16 1.90
309 315 5.601583 TTGGGATGCGTTATGTTACTAGA 57.398 39.130 0.00 0.00 0.00 2.43
327 333 4.511082 CCACATAAGCAAACTTGTTTTGGG 59.489 41.667 0.00 0.00 44.34 4.12
419 425 9.844790 TTTATTTGCTCATAGACTCAACATTTG 57.155 29.630 0.00 0.00 0.00 2.32
425 431 9.265901 GCTCTATTTATTTGCTCATAGACTCAA 57.734 33.333 0.00 0.00 0.00 3.02
435 441 9.657121 GTCATAAGTTGCTCTATTTATTTGCTC 57.343 33.333 0.00 0.00 0.00 4.26
437 443 9.226345 GTGTCATAAGTTGCTCTATTTATTTGC 57.774 33.333 0.00 0.00 0.00 3.68
448 454 8.883731 ACATAATAGTTGTGTCATAAGTTGCTC 58.116 33.333 0.00 0.00 28.01 4.26
525 531 9.413734 GTTATAGTGGGGAGTAACTTAGACTAA 57.586 37.037 0.00 0.00 0.00 2.24
545 551 4.945246 ACGTGACATAAGGCTGGTTATAG 58.055 43.478 0.00 0.00 0.00 1.31
546 552 4.647853 AGACGTGACATAAGGCTGGTTATA 59.352 41.667 0.00 0.00 0.00 0.98
547 553 3.451178 AGACGTGACATAAGGCTGGTTAT 59.549 43.478 0.00 0.00 0.00 1.89
548 554 2.829720 AGACGTGACATAAGGCTGGTTA 59.170 45.455 0.00 0.00 0.00 2.85
549 555 1.623811 AGACGTGACATAAGGCTGGTT 59.376 47.619 0.00 0.00 0.00 3.67
550 556 1.204941 GAGACGTGACATAAGGCTGGT 59.795 52.381 0.00 0.00 0.00 4.00
551 557 1.799181 CGAGACGTGACATAAGGCTGG 60.799 57.143 0.00 0.00 0.00 4.85
552 558 1.132453 TCGAGACGTGACATAAGGCTG 59.868 52.381 0.00 0.00 0.00 4.85
553 559 1.460504 TCGAGACGTGACATAAGGCT 58.539 50.000 0.00 0.00 0.00 4.58
554 560 2.120232 CATCGAGACGTGACATAAGGC 58.880 52.381 0.00 0.00 0.00 4.35
555 561 3.108881 CACATCGAGACGTGACATAAGG 58.891 50.000 0.00 0.00 35.02 2.69
556 562 2.531912 GCACATCGAGACGTGACATAAG 59.468 50.000 14.57 0.00 35.02 1.73
557 563 2.163613 AGCACATCGAGACGTGACATAA 59.836 45.455 14.57 0.00 35.02 1.90
558 564 1.743394 AGCACATCGAGACGTGACATA 59.257 47.619 14.57 0.00 35.02 2.29
559 565 0.528017 AGCACATCGAGACGTGACAT 59.472 50.000 14.57 0.00 35.02 3.06
560 566 0.313987 AAGCACATCGAGACGTGACA 59.686 50.000 14.57 0.00 35.02 3.58
561 567 1.419374 AAAGCACATCGAGACGTGAC 58.581 50.000 14.57 7.37 35.02 3.67
562 568 2.863739 CTAAAGCACATCGAGACGTGA 58.136 47.619 14.57 0.00 35.02 4.35
563 569 1.321743 GCTAAAGCACATCGAGACGTG 59.678 52.381 0.00 7.79 41.59 4.49
564 570 1.630148 GCTAAAGCACATCGAGACGT 58.370 50.000 0.00 0.00 41.59 4.34
565 571 0.567968 CGCTAAAGCACATCGAGACG 59.432 55.000 2.44 0.00 42.21 4.18
566 572 1.909376 TCGCTAAAGCACATCGAGAC 58.091 50.000 2.44 0.00 42.21 3.36
567 573 2.647529 TTCGCTAAAGCACATCGAGA 57.352 45.000 2.44 0.00 42.21 4.04
568 574 3.123621 AGTTTTCGCTAAAGCACATCGAG 59.876 43.478 2.44 0.00 42.21 4.04
569 575 3.064207 AGTTTTCGCTAAAGCACATCGA 58.936 40.909 2.44 0.00 42.21 3.59
570 576 3.155998 CAGTTTTCGCTAAAGCACATCG 58.844 45.455 2.44 0.00 42.21 3.84
571 577 4.147219 ACAGTTTTCGCTAAAGCACATC 57.853 40.909 2.44 0.00 42.21 3.06
572 578 4.568152 AACAGTTTTCGCTAAAGCACAT 57.432 36.364 2.44 0.00 42.21 3.21
573 579 5.487153 TTAACAGTTTTCGCTAAAGCACA 57.513 34.783 2.44 0.00 42.21 4.57
574 580 6.799786 TTTTAACAGTTTTCGCTAAAGCAC 57.200 33.333 2.44 0.00 42.21 4.40
617 623 0.370273 GCGCACATACGACTTCCAAG 59.630 55.000 0.30 0.00 34.06 3.61
622 628 1.141645 TTTTCGCGCACATACGACTT 58.858 45.000 8.75 0.00 38.17 3.01
661 667 0.320946 CTTTGCAGGGCCACCAATTG 60.321 55.000 6.18 0.00 40.13 2.32
667 673 0.032540 CAAAGTCTTTGCAGGGCCAC 59.967 55.000 12.26 0.00 33.36 5.01
748 754 1.468736 GCGACCCGTTAACCTAGTGAG 60.469 57.143 0.00 0.00 0.00 3.51
773 779 1.004918 GGTTCCACGTGGAGACCAG 60.005 63.158 37.35 17.57 46.36 4.00
823 829 1.806542 GACCATTCGCTGTGTGTGATT 59.193 47.619 0.00 0.00 34.87 2.57
826 832 0.943673 TTGACCATTCGCTGTGTGTG 59.056 50.000 0.00 0.00 0.00 3.82
827 833 1.806542 GATTGACCATTCGCTGTGTGT 59.193 47.619 0.00 0.00 0.00 3.72
828 834 1.805943 TGATTGACCATTCGCTGTGTG 59.194 47.619 0.00 0.00 0.00 3.82
829 835 2.183478 TGATTGACCATTCGCTGTGT 57.817 45.000 0.00 0.00 0.00 3.72
888 894 3.289407 AGGAGAGCCTTTAATTGGAGC 57.711 47.619 0.00 0.00 43.90 4.70
902 908 0.972134 TGTGGAGCAACTGAGGAGAG 59.028 55.000 0.00 0.00 0.00 3.20
954 960 1.203013 AGTGGGGGTTTGCTTAAGGTC 60.203 52.381 4.29 0.00 0.00 3.85
985 991 2.589540 CATGGCCGGCTCCAACTA 59.410 61.111 28.56 4.57 39.96 2.24
1207 1213 1.569493 CCAAGAAGACGCGGTTGTG 59.431 57.895 12.47 4.11 0.00 3.33
1768 1774 4.508128 GGAGATCGCGGCGACCAA 62.508 66.667 28.88 5.43 39.18 3.67
1961 1967 3.593442 TGTGATTCTTGGAAACAGGGT 57.407 42.857 0.00 0.00 44.54 4.34
1967 1973 7.654022 AAACTAACCTTGTGATTCTTGGAAA 57.346 32.000 0.00 0.00 0.00 3.13
2060 2100 5.855740 AGTACTGGTCAGGTAAGAATAGC 57.144 43.478 0.00 0.00 0.00 2.97
2072 3176 6.367374 TGGACATGAAAATAGTACTGGTCA 57.633 37.500 5.39 4.00 0.00 4.02
2073 3177 6.201044 CGATGGACATGAAAATAGTACTGGTC 59.799 42.308 5.39 0.00 0.00 4.02
2074 3178 6.049149 CGATGGACATGAAAATAGTACTGGT 58.951 40.000 5.39 0.00 0.00 4.00
2075 3179 5.466728 CCGATGGACATGAAAATAGTACTGG 59.533 44.000 5.39 0.00 0.00 4.00
2076 3180 5.050091 GCCGATGGACATGAAAATAGTACTG 60.050 44.000 5.39 0.00 0.00 2.74
2089 3193 0.916086 TTAACCAGGCCGATGGACAT 59.084 50.000 17.65 6.10 43.57 3.06
2185 3298 0.741915 GGGAGAGAAAGATCGAGCGT 59.258 55.000 0.00 0.00 0.00 5.07
2279 3393 8.507249 GTGTTACTTTTGATTGCTAGATCTTGT 58.493 33.333 0.00 0.00 0.00 3.16
2315 3434 2.175202 GAGCAGAACTTCTGGGAGAGA 58.825 52.381 18.53 0.00 44.43 3.10
2345 3464 6.142818 ACAAACCGAGATTGATTTTGTTCA 57.857 33.333 0.00 0.00 37.13 3.18
2361 3480 5.153513 CAACCACAGATATTTGACAAACCG 58.846 41.667 1.94 0.00 0.00 4.44
2474 3595 6.260714 GGATGGTGCTTTTCTTGTTTTTCATT 59.739 34.615 0.00 0.00 0.00 2.57
2475 3596 5.759763 GGATGGTGCTTTTCTTGTTTTTCAT 59.240 36.000 0.00 0.00 0.00 2.57
2476 3597 5.115480 GGATGGTGCTTTTCTTGTTTTTCA 58.885 37.500 0.00 0.00 0.00 2.69
2477 3598 4.209080 CGGATGGTGCTTTTCTTGTTTTTC 59.791 41.667 0.00 0.00 0.00 2.29
2511 3632 7.660208 ACAACACGGTTCTTCACTAGAAAATAT 59.340 33.333 0.00 0.00 44.25 1.28
2519 3640 5.336690 GGGTATACAACACGGTTCTTCACTA 60.337 44.000 5.01 0.00 0.00 2.74
2556 3677 9.847224 TGTCCAGGAGTCTAATTAATAAAATCC 57.153 33.333 0.00 0.00 0.00 3.01
2595 3718 4.023365 AGCTGAAAGTGCAGATCAAGAAAC 60.023 41.667 0.00 0.00 38.14 2.78
2609 3732 6.645790 AGAAAATGTTGATGAGCTGAAAGT 57.354 33.333 0.00 0.00 35.30 2.66
2643 3766 4.468510 TGTATCTTGGACCACGATTACCTT 59.531 41.667 17.82 0.00 0.00 3.50
2689 3812 9.932699 TTTCAACAGTTGCATCAATTTATTTTG 57.067 25.926 8.58 0.00 0.00 2.44
2825 3950 9.708222 GATTGCTTAACAGTATGAACATTAGTG 57.292 33.333 0.00 0.00 39.69 2.74
2839 3964 3.935203 AGACATGGACGATTGCTTAACAG 59.065 43.478 0.00 0.00 0.00 3.16
2862 3987 3.563808 TGGTGCTGTGTGACAAATAGTTC 59.436 43.478 0.00 0.00 0.00 3.01
2879 4004 2.048877 GTTGCTGCATGGTGGTGC 60.049 61.111 1.84 0.00 45.25 5.01
2880 4005 0.319083 AATGTTGCTGCATGGTGGTG 59.681 50.000 1.84 0.00 0.00 4.17
2925 4050 1.661341 GGCGCACAAGAGATCAATCT 58.339 50.000 10.83 0.00 40.50 2.40
2975 4100 0.460284 CCGTCTAGGGTGCACATGAC 60.460 60.000 20.43 17.52 35.97 3.06
2989 4114 2.683933 AATGGGGCGTCTCCGTCT 60.684 61.111 0.00 0.00 39.11 4.18
2991 4116 4.778143 GCAATGGGGCGTCTCCGT 62.778 66.667 0.00 0.00 36.15 4.69
3106 4232 5.640357 CAGTTTTCATGGAAAATCACATGGG 59.360 40.000 0.00 0.00 42.31 4.00
3108 4234 9.642327 TTATCAGTTTTCATGGAAAATCACATG 57.358 29.630 0.00 0.00 42.31 3.21
3128 4254 7.070571 TGGGGCCTTTTTAATATTGGTTATCAG 59.929 37.037 0.84 0.00 0.00 2.90
3130 4256 7.368198 TGGGGCCTTTTTAATATTGGTTATC 57.632 36.000 0.84 0.00 0.00 1.75
3131 4257 7.404688 ACTTGGGGCCTTTTTAATATTGGTTAT 59.595 33.333 0.84 0.00 0.00 1.89
3132 4258 6.731448 ACTTGGGGCCTTTTTAATATTGGTTA 59.269 34.615 0.84 0.00 0.00 2.85
3147 4273 4.339335 AGTCAAGACTTGGGGCCT 57.661 55.556 15.13 4.00 38.83 5.19
3179 4305 1.521681 GGCCGGTCCTGAGATTTCG 60.522 63.158 1.90 0.00 0.00 3.46
3180 4306 1.153147 GGGCCGGTCCTGAGATTTC 60.153 63.158 20.78 0.00 34.39 2.17
3194 4320 4.554036 GAGGGTGCGATCAGGGCC 62.554 72.222 0.00 0.00 0.00 5.80
3195 4321 3.785859 TGAGGGTGCGATCAGGGC 61.786 66.667 0.00 0.00 0.00 5.19
3196 4322 2.187946 GTGAGGGTGCGATCAGGG 59.812 66.667 0.00 0.00 0.00 4.45
3197 4323 2.184020 TTGGTGAGGGTGCGATCAGG 62.184 60.000 0.00 0.00 0.00 3.86
3198 4324 0.321564 TTTGGTGAGGGTGCGATCAG 60.322 55.000 0.00 0.00 0.00 2.90
3199 4325 0.605319 GTTTGGTGAGGGTGCGATCA 60.605 55.000 0.00 0.00 0.00 2.92
3200 4326 0.605319 TGTTTGGTGAGGGTGCGATC 60.605 55.000 0.00 0.00 0.00 3.69
3214 4340 1.837747 GTGCTGTCGTTTTCGTGTTTG 59.162 47.619 0.00 0.00 44.46 2.93
3215 4341 1.735571 AGTGCTGTCGTTTTCGTGTTT 59.264 42.857 0.00 0.00 44.46 2.83
3241 4367 2.930950 TGCTGGTACTTGAAGCAAACT 58.069 42.857 9.56 0.00 43.65 2.66
3346 4472 2.627699 TGGAAACCACAGGAAATGAAGC 59.372 45.455 0.00 0.00 0.00 3.86
3373 4499 3.577415 AGTTGGTAGGAGTAGGTGACAAC 59.423 47.826 0.00 0.00 37.73 3.32
3429 4555 2.036256 ACCATGTTGAGCAGCCCC 59.964 61.111 0.00 0.00 0.00 5.80
3690 4816 0.749649 CGGTCATAAGCAGCCTCTCT 59.250 55.000 0.00 0.00 0.00 3.10
3727 4853 2.028190 CTTCGCGGCCATCTCGAT 59.972 61.111 6.13 0.00 31.96 3.59
3765 4891 3.861797 CCATCTTCCCCGGTCCCG 61.862 72.222 0.00 0.00 39.44 5.14
3904 5030 4.988716 ACGTCGCCCTGTCCCTGA 62.989 66.667 0.00 0.00 0.00 3.86
3988 5114 8.832735 TGGATACTGAAGTTTTATTTAGACCCT 58.167 33.333 0.00 0.00 37.61 4.34
4114 5247 0.677098 CCTCCGAGAGACTGAACCGA 60.677 60.000 0.00 0.00 0.00 4.69
4118 5251 0.251386 AGCACCTCCGAGAGACTGAA 60.251 55.000 0.00 0.00 0.00 3.02
4130 5263 4.586841 ACACCTTATCTCTATGAGCACCTC 59.413 45.833 0.00 0.00 0.00 3.85
4143 5276 4.019792 TGAATGCACACACACCTTATCT 57.980 40.909 0.00 0.00 0.00 1.98
4144 5277 4.970662 ATGAATGCACACACACCTTATC 57.029 40.909 0.00 0.00 0.00 1.75
4145 5278 5.357878 CCTTATGAATGCACACACACCTTAT 59.642 40.000 0.00 0.00 0.00 1.73
4148 5281 3.084039 CCTTATGAATGCACACACACCT 58.916 45.455 0.00 0.00 0.00 4.00
4150 5283 4.395854 TCATCCTTATGAATGCACACACAC 59.604 41.667 0.00 0.00 39.20 3.82
4158 6082 7.918536 ATCATACACTCATCCTTATGAATGC 57.081 36.000 0.00 0.00 41.91 3.56
4181 6105 6.419116 CAGACGCAAGCGCTCATATATATAAT 59.581 38.462 12.06 0.00 44.19 1.28
4182 6106 5.743872 CAGACGCAAGCGCTCATATATATAA 59.256 40.000 12.06 0.00 44.19 0.98
4222 6148 0.255033 GGGGAGGTTCCACATACCAC 59.745 60.000 0.00 0.00 40.54 4.16
4223 6149 0.120377 AGGGGAGGTTCCACATACCA 59.880 55.000 0.00 0.00 44.30 3.25
4228 6155 2.352561 TTATGAGGGGAGGTTCCACA 57.647 50.000 0.00 0.00 44.30 4.17
4249 6176 3.066380 GGTTCCGCGTACCTTCTTTTTA 58.934 45.455 17.56 0.00 32.75 1.52
4253 6180 0.611714 ATGGTTCCGCGTACCTTCTT 59.388 50.000 23.03 7.73 36.60 2.52
4254 6181 1.477553 TATGGTTCCGCGTACCTTCT 58.522 50.000 23.03 13.14 36.60 2.85
4264 6191 4.498009 GCATGGACAATCTTTATGGTTCCG 60.498 45.833 0.00 0.00 0.00 4.30
4279 6206 1.906105 GAAGGGGTACGGCATGGACA 61.906 60.000 0.00 0.00 0.00 4.02
4346 6273 4.379243 CGGACTGGCAGCGTTCCT 62.379 66.667 15.89 0.00 0.00 3.36
4393 6322 4.814294 GCCGAGATCCGCCGTGTT 62.814 66.667 0.00 0.00 36.84 3.32
4399 6328 1.079750 GATAAGGGCCGAGATCCGC 60.080 63.158 0.00 0.00 36.84 5.54
4400 6329 0.244994 CTGATAAGGGCCGAGATCCG 59.755 60.000 0.00 0.00 38.18 4.18
4449 6384 7.661437 AGCATGACACAAACTCTAACAAGATTA 59.339 33.333 0.00 0.00 0.00 1.75
4451 6386 6.000219 AGCATGACACAAACTCTAACAAGAT 59.000 36.000 0.00 0.00 0.00 2.40
4477 6413 0.249447 CATCGCTGCCTCGTATTCCA 60.249 55.000 0.00 0.00 0.00 3.53
4482 6418 2.309528 AAAATCATCGCTGCCTCGTA 57.690 45.000 0.00 0.00 0.00 3.43
4543 6485 1.819903 GACGAGGCTAGAAACTCCACT 59.180 52.381 0.28 0.00 0.00 4.00
4548 6490 1.473278 CCTTCGACGAGGCTAGAAACT 59.527 52.381 0.28 0.00 0.00 2.66
4558 6500 2.805353 CACACGCCCTTCGACGAG 60.805 66.667 0.00 0.00 41.67 4.18
4690 6632 3.304257 CCGATGAAGAGAAGCGTAGATG 58.696 50.000 0.00 0.00 0.00 2.90
4733 6675 4.037927 TGCTAAGGCCTTATAGAACCAGT 58.962 43.478 25.37 0.00 37.74 4.00
4744 6687 1.080025 GTCGTCGTGCTAAGGCCTT 60.080 57.895 24.18 24.18 37.74 4.35
4788 6731 4.409570 CTCATTGATTGAAACCGAGCAAG 58.590 43.478 0.00 0.00 32.78 4.01
4801 6744 2.477825 CGTCATCGCTCCTCATTGATT 58.522 47.619 0.00 0.00 0.00 2.57
4862 6805 5.881923 TTCAGGTTTGTAGAACACCTAGT 57.118 39.130 6.28 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.