Multiple sequence alignment - TraesCS6B01G112400

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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 TraesCS6B01G112400 chr6B 100.000 4334 0 0 1 4334 93996731 94001064 0.000000e+00 8004.0
1 TraesCS6B01G112400 chr6B 76.667 240 44 7 17 246 237102424 237102187 5.890000e-24 122.0
2 TraesCS6B01G112400 chr6A 90.936 2041 95 33 1814 3814 58149284 58151274 0.000000e+00 2662.0
3 TraesCS6B01G112400 chr6A 93.808 969 27 11 835 1778 58148331 58149291 0.000000e+00 1426.0
4 TraesCS6B01G112400 chr6A 83.333 510 53 19 268 760 58146636 58147130 3.980000e-120 442.0
5 TraesCS6B01G112400 chr6A 91.429 70 6 0 6 75 58104979 58105048 3.570000e-16 97.1
6 TraesCS6B01G112400 chr6D 94.975 1612 53 13 842 2429 42566985 42565378 0.000000e+00 2503.0
7 TraesCS6B01G112400 chr6D 89.578 1468 77 23 2425 3853 42565250 42563820 0.000000e+00 1794.0
8 TraesCS6B01G112400 chr6D 86.111 360 41 8 3879 4236 42563754 42563402 3.160000e-101 379.0
9 TraesCS6B01G112400 chrUn 82.064 814 91 24 7 787 18793423 18792632 1.020000e-180 643.0
10 TraesCS6B01G112400 chr3B 79.077 607 99 19 1 601 35973546 35974130 4.060000e-105 392.0
11 TraesCS6B01G112400 chr3B 83.962 106 14 2 499 603 398847129 398847232 9.920000e-17 99.0
12 TraesCS6B01G112400 chr3A 77.483 604 74 27 23 600 451672581 451673148 5.450000e-79 305.0
13 TraesCS6B01G112400 chr3A 91.304 92 6 2 4244 4334 232433791 232433701 1.640000e-24 124.0
14 TraesCS6B01G112400 chr3A 84.466 103 12 3 505 605 494804572 494804472 9.920000e-17 99.0
15 TraesCS6B01G112400 chr7A 75.490 612 121 22 1 601 533902533 533901940 5.520000e-69 272.0
16 TraesCS6B01G112400 chr7A 100.000 31 0 0 24 54 86244592 86244562 1.680000e-04 58.4
17 TraesCS6B01G112400 chr1D 80.645 310 47 10 295 601 166840851 166841150 1.210000e-55 228.0
18 TraesCS6B01G112400 chr4D 77.695 269 34 13 1 246 396936398 396936663 1.620000e-29 141.0
19 TraesCS6B01G112400 chr5D 88.119 101 9 2 503 602 160875265 160875363 2.740000e-22 117.0
20 TraesCS6B01G112400 chr2D 87.629 97 6 5 510 603 300432433 300432526 1.650000e-19 108.0
21 TraesCS6B01G112400 chr5B 87.234 94 9 2 510 602 317300581 317300672 2.130000e-18 104.0
22 TraesCS6B01G112400 chr1A 85.437 103 12 2 505 606 350415743 350415643 2.130000e-18 104.0
23 TraesCS6B01G112400 chr2B 85.000 100 12 2 505 603 188256323 188256226 9.920000e-17 99.0
24 TraesCS6B01G112400 chr1B 83.654 104 14 2 505 607 647917750 647917649 1.280000e-15 95.3


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 TraesCS6B01G112400 chr6B 93996731 94001064 4333 False 8004.000000 8004 100.000000 1 4334 1 chr6B.!!$F1 4333
1 TraesCS6B01G112400 chr6A 58146636 58151274 4638 False 1510.000000 2662 89.359000 268 3814 3 chr6A.!!$F2 3546
2 TraesCS6B01G112400 chr6D 42563402 42566985 3583 True 1558.666667 2503 90.221333 842 4236 3 chr6D.!!$R1 3394
3 TraesCS6B01G112400 chrUn 18792632 18793423 791 True 643.000000 643 82.064000 7 787 1 chrUn.!!$R1 780
4 TraesCS6B01G112400 chr3B 35973546 35974130 584 False 392.000000 392 79.077000 1 601 1 chr3B.!!$F1 600
5 TraesCS6B01G112400 chr3A 451672581 451673148 567 False 305.000000 305 77.483000 23 600 1 chr3A.!!$F1 577
6 TraesCS6B01G112400 chr7A 533901940 533902533 593 True 272.000000 272 75.490000 1 601 1 chr7A.!!$R2 600

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
923 2163 0.389426 TAAACGAGTGCGAGCCTTCC 60.389 55.0 0.00 0.0 41.64 3.46 F
949 2199 0.637195 CCCTTCCTCCTCCTCTACCA 59.363 60.0 0.00 0.0 0.00 3.25 F
1921 3182 0.837272 ATAGACACCCGGTTGGATGG 59.163 55.0 3.27 0.0 37.49 3.51 F
3221 4636 0.251916 CTCCCATGGCTAACCGTTGA 59.748 55.0 6.09 0.0 39.70 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 3417 0.037303 CCAGTGGAGAACCTGCATGT 59.963 55.000 1.68 0.0 33.78 3.21 R
2610 4002 2.936498 ACACAAACACAGAAGAGTTCGG 59.064 45.455 0.00 0.0 34.02 4.30 R
3228 4643 0.535780 TGTCCTGCAACAGCAAGGAG 60.536 55.000 8.28 0.0 37.91 3.69 R
4076 5568 0.324923 ATGATGCACCTGCCCAACAT 60.325 50.000 0.00 0.0 41.18 2.71 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
138 159 1.735571 GCGTTTCTCGGGCAAGAAATA 59.264 47.619 14.78 0.00 44.64 1.40
149 170 4.536765 GGGCAAGAAATAAATCTCCCAGA 58.463 43.478 0.00 0.00 34.86 3.86
164 185 4.078336 TCTCCCAGATGAGGATTAGACCTT 60.078 45.833 0.00 0.00 40.73 3.50
182 203 2.507058 CCTTCCCTGTGAGGATTCATCA 59.493 50.000 0.00 0.00 37.67 3.07
200 222 1.067669 TCATCGCCGAAGAGGATTCAG 59.932 52.381 0.00 0.00 45.00 3.02
222 244 2.600420 CCACTCTGATGACAAATCGACG 59.400 50.000 0.00 0.00 0.00 5.12
240 262 0.464036 CGGATTTCGGAGTGGGATCA 59.536 55.000 0.00 0.00 34.75 2.92
248 270 3.572642 TCGGAGTGGGATCAAGCTTATA 58.427 45.455 0.00 0.00 0.00 0.98
284 306 2.027192 GCTTCACTGACTGGTTCCCATA 60.027 50.000 0.00 0.00 30.82 2.74
315 349 0.618968 GGGCAGAGGAAGAGGGAGAA 60.619 60.000 0.00 0.00 0.00 2.87
334 369 0.523072 AAGCGACATCATGCACCAAC 59.477 50.000 0.00 0.00 0.00 3.77
340 398 3.076621 GACATCATGCACCAACAGAGAA 58.923 45.455 0.00 0.00 0.00 2.87
348 406 0.402121 ACCAACAGAGAAAGAGGGCC 59.598 55.000 0.00 0.00 0.00 5.80
352 410 0.474660 ACAGAGAAAGAGGGCCAGGT 60.475 55.000 6.18 0.00 0.00 4.00
372 430 2.123854 ATAGGCGGCGTGAGGAGA 60.124 61.111 9.37 0.00 0.00 3.71
386 444 5.390991 GCGTGAGGAGAAAACCTAGATTTTG 60.391 44.000 0.00 0.00 40.73 2.44
396 454 7.929785 AGAAAACCTAGATTTTGTTGTCGACTA 59.070 33.333 17.92 6.32 32.63 2.59
400 458 5.580691 CCTAGATTTTGTTGTCGACTATGCA 59.419 40.000 17.92 7.40 0.00 3.96
418 479 1.588674 CACACACACGGGAGCTTTAA 58.411 50.000 0.00 0.00 0.00 1.52
458 519 1.445871 CCTGTGGTTTAACGGGCTAC 58.554 55.000 0.00 0.00 39.70 3.58
476 539 2.922950 CGCCGGCCCGTATAGCTTA 61.923 63.158 23.46 0.00 0.00 3.09
479 542 1.609841 GCCGGCCCGTATAGCTTATTT 60.610 52.381 18.11 0.00 0.00 1.40
480 543 2.344025 CCGGCCCGTATAGCTTATTTC 58.656 52.381 0.85 0.00 0.00 2.17
481 544 2.028385 CCGGCCCGTATAGCTTATTTCT 60.028 50.000 0.85 0.00 0.00 2.52
487 550 5.526111 GCCCGTATAGCTTATTTCTTTCACA 59.474 40.000 0.00 0.00 0.00 3.58
513 576 3.559655 CAGTGCTAATGCCTAATTACGCA 59.440 43.478 10.89 10.89 39.79 5.24
519 582 7.271223 GTGCTAATGCCTAATTACGCATAATTG 59.729 37.037 18.42 9.13 44.80 2.32
520 583 6.251376 GCTAATGCCTAATTACGCATAATTGC 59.749 38.462 18.42 13.58 44.80 3.56
542 606 5.883328 CGCTAATCGTGCATAAGTTAGAA 57.117 39.130 12.42 0.00 0.00 2.10
577 641 3.130340 AGGTGGCCAAACGCATAATTAAG 59.870 43.478 7.24 0.00 40.31 1.85
655 737 8.836413 CATTATGTGACTAAAACATATCCGGTT 58.164 33.333 0.00 0.00 39.57 4.44
812 894 8.812513 ATTTTCATCATGGTAGATCTTTCACA 57.187 30.769 0.00 0.00 0.00 3.58
813 895 7.615582 TTTCATCATGGTAGATCTTTCACAC 57.384 36.000 0.00 0.00 0.00 3.82
814 896 6.298441 TCATCATGGTAGATCTTTCACACA 57.702 37.500 0.00 0.00 0.00 3.72
815 897 6.710278 TCATCATGGTAGATCTTTCACACAA 58.290 36.000 0.00 0.00 0.00 3.33
816 898 6.820152 TCATCATGGTAGATCTTTCACACAAG 59.180 38.462 0.00 0.00 0.00 3.16
818 900 6.533730 TCATGGTAGATCTTTCACACAAGTT 58.466 36.000 0.00 0.00 0.00 2.66
819 901 6.998074 TCATGGTAGATCTTTCACACAAGTTT 59.002 34.615 0.00 0.00 0.00 2.66
888 2128 4.641989 CCATCCCGAATCTCAAAGACAAAT 59.358 41.667 0.00 0.00 0.00 2.32
922 2162 0.992802 CTAAACGAGTGCGAGCCTTC 59.007 55.000 0.00 0.00 41.64 3.46
923 2163 0.389426 TAAACGAGTGCGAGCCTTCC 60.389 55.000 0.00 0.00 41.64 3.46
949 2199 0.637195 CCCTTCCTCCTCCTCTACCA 59.363 60.000 0.00 0.00 0.00 3.25
1059 2309 2.792599 CTCCTCTTCCCGTCGTCG 59.207 66.667 0.00 0.00 0.00 5.12
1062 2312 2.484203 CTCTTCCCGTCGTCGTCC 59.516 66.667 0.71 0.00 35.01 4.79
1294 2546 3.274095 AGCTGGGCTAAAATCTCTCAC 57.726 47.619 0.00 0.00 36.99 3.51
1384 2636 2.803956 CGGTTCTGACGTTTATTGGTGT 59.196 45.455 0.00 0.00 0.00 4.16
1436 2691 4.901197 TGAGTACCACCACAACATGTAT 57.099 40.909 0.00 0.00 0.00 2.29
1547 2802 3.284323 ACCGTCTTATATGCTAGTGCG 57.716 47.619 0.00 0.00 43.34 5.34
1788 3049 1.879380 TCTTGTTGACTTGAATGCCGG 59.121 47.619 0.00 0.00 0.00 6.13
1799 3060 4.876107 ACTTGAATGCCGGTTCTATGTTAG 59.124 41.667 1.90 0.00 0.00 2.34
1815 3076 9.767684 TTCTATGTTAGTGCAAATTTACGATTG 57.232 29.630 0.00 0.00 0.00 2.67
1819 3080 8.276060 TGTTAGTGCAAATTTACGATTGTTTC 57.724 30.769 0.00 0.00 0.00 2.78
1869 3130 9.013229 TGATAACACAAATTGACTTGAGCTTAT 57.987 29.630 0.00 0.00 0.00 1.73
1920 3181 1.953559 CATAGACACCCGGTTGGATG 58.046 55.000 3.27 0.14 37.49 3.51
1921 3182 0.837272 ATAGACACCCGGTTGGATGG 59.163 55.000 3.27 0.00 37.49 3.51
2061 3322 2.866762 GCGAGGTCACTAGGCTTTAATG 59.133 50.000 0.00 0.00 0.00 1.90
2081 3342 6.749923 AATGTTGCAAGAGGAGAGATTTAC 57.250 37.500 0.00 0.00 0.00 2.01
2082 3343 5.489792 TGTTGCAAGAGGAGAGATTTACT 57.510 39.130 0.00 0.00 0.00 2.24
2156 3417 8.084684 GCTCGCATGGTGATATCATATTATCTA 58.915 37.037 9.02 0.00 31.19 1.98
2335 3596 1.211457 CTTGGAGATAGGCACCTTGCT 59.789 52.381 0.00 0.00 44.28 3.91
2362 3623 5.713861 ACAATTTCAGGAAATTCCTCTGGAG 59.286 40.000 12.35 0.48 45.66 3.86
2422 3683 6.938030 AGTTTCACGTTTAGAATGGTTCCATA 59.062 34.615 4.67 0.00 0.00 2.74
2423 3684 6.730960 TTCACGTTTAGAATGGTTCCATAC 57.269 37.500 4.67 0.00 0.00 2.39
2424 3685 5.795972 TCACGTTTAGAATGGTTCCATACA 58.204 37.500 4.67 0.00 0.00 2.29
2425 3686 6.411376 TCACGTTTAGAATGGTTCCATACAT 58.589 36.000 4.67 0.00 0.00 2.29
2426 3687 6.315144 TCACGTTTAGAATGGTTCCATACATG 59.685 38.462 4.67 0.00 0.00 3.21
2427 3688 6.093495 CACGTTTAGAATGGTTCCATACATGT 59.907 38.462 2.69 2.69 0.00 3.21
2428 3689 7.279090 CACGTTTAGAATGGTTCCATACATGTA 59.721 37.037 8.27 8.27 0.00 2.29
2429 3690 7.825270 ACGTTTAGAATGGTTCCATACATGTAA 59.175 33.333 10.14 0.00 0.00 2.41
2557 3949 9.941325 AATGAGGTATTCTAAGCATCTATGAAG 57.059 33.333 0.00 0.00 0.00 3.02
2558 3950 8.712228 TGAGGTATTCTAAGCATCTATGAAGA 57.288 34.615 0.00 0.00 35.80 2.87
2572 3964 6.560253 TCTATGAAGAAACAAAAGCCTGAC 57.440 37.500 0.00 0.00 0.00 3.51
2573 3965 6.061441 TCTATGAAGAAACAAAAGCCTGACA 58.939 36.000 0.00 0.00 0.00 3.58
2577 3969 5.360714 TGAAGAAACAAAAGCCTGACAAGAT 59.639 36.000 0.00 0.00 0.00 2.40
2589 3981 5.645497 AGCCTGACAAGATGTTCAATAACTC 59.355 40.000 0.00 0.00 36.51 3.01
2590 3982 5.412594 GCCTGACAAGATGTTCAATAACTCA 59.587 40.000 0.00 0.00 36.51 3.41
2603 3995 7.119699 TGTTCAATAACTCATCTGCCAGTAAAG 59.880 37.037 0.00 0.00 36.51 1.85
2610 4002 5.239525 ACTCATCTGCCAGTAAAGTTGAAAC 59.760 40.000 0.00 0.00 0.00 2.78
2611 4003 4.518970 TCATCTGCCAGTAAAGTTGAAACC 59.481 41.667 0.00 0.00 0.00 3.27
2624 4029 3.871594 AGTTGAAACCGAACTCTTCTGTG 59.128 43.478 0.00 0.00 0.00 3.66
2669 4074 5.543790 ACTGGCAATTTTAGTGGAAGGATTT 59.456 36.000 0.00 0.00 0.00 2.17
2722 4128 7.938563 TTTCATTTGCATTAGTTTGGTACAC 57.061 32.000 0.00 0.00 39.29 2.90
2729 4135 8.487313 TTGCATTAGTTTGGTACACTAGTATG 57.513 34.615 0.00 0.00 39.29 2.39
2793 4199 6.199342 GGCGTCTTCAGAAATAGTATCTGTTC 59.801 42.308 3.72 0.00 43.77 3.18
2983 4395 4.083537 CGTAAGAAATTGTGCTGCCACTTA 60.084 41.667 0.00 0.00 40.86 2.24
3195 4610 4.102996 TCCTGTGCTGATAAATGGCTATCA 59.897 41.667 0.00 0.00 36.22 2.15
3208 4623 2.785269 TGGCTATCATGGTTTCTCCCAT 59.215 45.455 0.00 0.00 46.28 4.00
3221 4636 0.251916 CTCCCATGGCTAACCGTTGA 59.748 55.000 6.09 0.00 39.70 3.18
3228 4643 3.188159 TGGCTAACCGTTGACCATATC 57.812 47.619 3.58 0.00 39.70 1.63
3234 4649 3.543680 ACCGTTGACCATATCTCCTTG 57.456 47.619 0.00 0.00 0.00 3.61
3336 4751 0.609131 CCGCCCAAGTCCTGTGATTT 60.609 55.000 0.00 0.00 0.00 2.17
3337 4752 0.804989 CGCCCAAGTCCTGTGATTTC 59.195 55.000 0.00 0.00 0.00 2.17
3345 4760 3.679389 AGTCCTGTGATTTCCATGTGTC 58.321 45.455 0.00 0.00 0.00 3.67
3351 4766 3.629855 TGTGATTTCCATGTGTCGTTTGT 59.370 39.130 0.00 0.00 0.00 2.83
3358 4773 2.548057 CCATGTGTCGTTTGTGTAGCTT 59.452 45.455 0.00 0.00 0.00 3.74
3396 4819 1.852280 GTGCTTGGTTTTCGTTTGCTC 59.148 47.619 0.00 0.00 0.00 4.26
3441 4864 8.575589 TGTTGTCAGAATATGCATTTTTGTACT 58.424 29.630 3.54 0.00 0.00 2.73
3476 4899 5.779806 TCTAAAGAAAAGAATTCTCCGCG 57.220 39.130 8.78 0.00 0.00 6.46
3534 4957 6.318900 CCAGACCTTTCCATTGGATTTAGTAC 59.681 42.308 6.15 2.13 0.00 2.73
3535 4958 6.884295 CAGACCTTTCCATTGGATTTAGTACA 59.116 38.462 6.15 0.00 0.00 2.90
3536 4959 7.066284 CAGACCTTTCCATTGGATTTAGTACAG 59.934 40.741 6.15 0.00 0.00 2.74
3537 4960 6.790319 ACCTTTCCATTGGATTTAGTACAGT 58.210 36.000 6.15 0.00 0.00 3.55
3538 4961 7.924541 ACCTTTCCATTGGATTTAGTACAGTA 58.075 34.615 6.15 0.00 0.00 2.74
3539 4962 7.827729 ACCTTTCCATTGGATTTAGTACAGTAC 59.172 37.037 6.15 2.05 0.00 2.73
3560 4983 4.642429 ACTAGTACTTTGTTTCTGGCTGG 58.358 43.478 0.00 0.00 0.00 4.85
3580 5003 6.094603 GGCTGGATATTTGTAATGCCTGATAG 59.905 42.308 0.00 0.00 36.52 2.08
3586 5009 9.277783 GATATTTGTAATGCCTGATAGTTGTCT 57.722 33.333 0.00 0.00 0.00 3.41
3593 5016 3.196469 TGCCTGATAGTTGTCTGAGGAAG 59.804 47.826 0.00 0.00 0.00 3.46
3609 5032 1.742268 GGAAGAGTGAATGCTGGCTTC 59.258 52.381 0.00 0.00 0.00 3.86
3618 5042 2.712057 ATGCTGGCTTCGTTTTCTTG 57.288 45.000 0.00 0.00 0.00 3.02
3625 5049 1.604604 CTTCGTTTTCTTGGCTCCCA 58.395 50.000 0.00 0.00 0.00 4.37
3741 5166 5.040635 CCTTGAAACAAAAGCGTGTTGTAT 58.959 37.500 4.54 0.00 40.86 2.29
3742 5167 5.173131 CCTTGAAACAAAAGCGTGTTGTATC 59.827 40.000 4.54 0.90 40.86 2.24
3743 5168 4.275662 TGAAACAAAAGCGTGTTGTATCG 58.724 39.130 4.54 0.00 40.86 2.92
3744 5169 4.034163 TGAAACAAAAGCGTGTTGTATCGA 59.966 37.500 4.54 0.00 40.86 3.59
3745 5170 4.539509 AACAAAAGCGTGTTGTATCGAA 57.460 36.364 0.00 0.00 40.22 3.71
3746 5171 4.128554 ACAAAAGCGTGTTGTATCGAAG 57.871 40.909 0.00 0.00 37.44 3.79
3747 5172 3.805422 ACAAAAGCGTGTTGTATCGAAGA 59.195 39.130 0.00 0.00 37.44 2.87
3748 5173 4.271533 ACAAAAGCGTGTTGTATCGAAGAA 59.728 37.500 0.00 0.00 37.44 2.52
3749 5174 5.049680 ACAAAAGCGTGTTGTATCGAAGAAT 60.050 36.000 0.00 0.00 37.44 2.40
3853 5305 2.537625 GCTGACGTACATGAAGATGAGC 59.462 50.000 0.00 0.00 33.36 4.26
3855 5307 3.774066 TGACGTACATGAAGATGAGCTG 58.226 45.455 0.00 0.00 33.36 4.24
3856 5308 3.443681 TGACGTACATGAAGATGAGCTGA 59.556 43.478 0.00 0.00 33.36 4.26
3857 5309 4.039151 ACGTACATGAAGATGAGCTGAG 57.961 45.455 0.00 0.00 33.36 3.35
3858 5310 3.181482 ACGTACATGAAGATGAGCTGAGG 60.181 47.826 0.00 0.00 33.36 3.86
3860 5312 2.194859 ACATGAAGATGAGCTGAGGGT 58.805 47.619 0.00 0.00 33.36 4.34
3862 5314 2.775911 TGAAGATGAGCTGAGGGTTG 57.224 50.000 0.00 0.00 0.00 3.77
3863 5315 1.339438 TGAAGATGAGCTGAGGGTTGC 60.339 52.381 0.00 0.00 0.00 4.17
3864 5316 0.034670 AAGATGAGCTGAGGGTTGCC 60.035 55.000 0.00 0.00 0.00 4.52
3865 5317 1.203441 AGATGAGCTGAGGGTTGCCA 61.203 55.000 0.00 0.00 0.00 4.92
3866 5318 0.106819 GATGAGCTGAGGGTTGCCAT 60.107 55.000 0.00 0.00 0.00 4.40
3867 5319 0.395311 ATGAGCTGAGGGTTGCCATG 60.395 55.000 0.00 0.00 0.00 3.66
3868 5320 2.362120 AGCTGAGGGTTGCCATGC 60.362 61.111 0.00 0.00 0.00 4.06
3869 5321 3.455469 GCTGAGGGTTGCCATGCC 61.455 66.667 0.00 0.00 0.00 4.40
3876 5328 3.134127 GTTGCCATGCCCTCCGAC 61.134 66.667 0.00 0.00 0.00 4.79
3877 5329 4.424711 TTGCCATGCCCTCCGACC 62.425 66.667 0.00 0.00 0.00 4.79
3890 5382 2.969238 CGACCATGATCCAGCGGC 60.969 66.667 0.00 0.00 0.00 6.53
3891 5383 2.190313 GACCATGATCCAGCGGCA 59.810 61.111 1.45 0.00 0.00 5.69
3912 5404 4.500375 GCAGAGAGCAATTTGACCAAAACT 60.500 41.667 0.00 0.00 44.79 2.66
3954 5446 6.959606 AATCTGTAATAGTCTGCCCCATAT 57.040 37.500 0.00 0.00 0.00 1.78
3955 5447 5.745312 TCTGTAATAGTCTGCCCCATATG 57.255 43.478 0.00 0.00 0.00 1.78
3971 5463 6.539173 CCCCATATGTTTATGTAGTTAGCCA 58.461 40.000 1.24 0.00 34.54 4.75
3972 5464 6.430000 CCCCATATGTTTATGTAGTTAGCCAC 59.570 42.308 1.24 0.00 34.54 5.01
3980 5472 1.337447 TGTAGTTAGCCACGGTCAAGC 60.337 52.381 0.00 0.00 0.00 4.01
3983 5475 0.517316 GTTAGCCACGGTCAAGCTTG 59.483 55.000 20.81 20.81 38.06 4.01
4013 5505 3.058983 TGCATTGCTGTTTACAAGTCTCG 60.059 43.478 10.49 0.00 0.00 4.04
4016 5508 3.446310 TGCTGTTTACAAGTCTCGACA 57.554 42.857 0.00 0.00 0.00 4.35
4026 5518 5.907197 ACAAGTCTCGACAAACATGTAAG 57.093 39.130 0.00 0.00 0.00 2.34
4031 5523 2.416547 CTCGACAAACATGTAAGGCTGG 59.583 50.000 0.00 0.00 0.00 4.85
4042 5534 2.216898 GTAAGGCTGGTCATCATGAGC 58.783 52.381 10.07 10.07 44.54 4.26
4047 5539 1.129917 CTGGTCATCATGAGCCTCCT 58.870 55.000 14.30 0.00 43.72 3.69
4064 5556 2.480419 CTCCTGCGATCTTCGTTTGTTT 59.520 45.455 0.00 0.00 42.81 2.83
4065 5557 2.478894 TCCTGCGATCTTCGTTTGTTTC 59.521 45.455 0.00 0.00 42.81 2.78
4067 5559 2.128821 TGCGATCTTCGTTTGTTTCGA 58.871 42.857 0.00 0.00 42.81 3.71
4074 5566 6.573725 CGATCTTCGTTTGTTTCGATCTTTTT 59.426 34.615 0.00 0.00 37.18 1.94
4075 5567 7.738609 CGATCTTCGTTTGTTTCGATCTTTTTA 59.261 33.333 0.00 0.00 37.18 1.52
4076 5568 9.377383 GATCTTCGTTTGTTTCGATCTTTTTAA 57.623 29.630 0.00 0.00 37.18 1.52
4080 5572 8.844441 TCGTTTGTTTCGATCTTTTTAATGTT 57.156 26.923 0.00 0.00 32.30 2.71
4094 5586 0.542467 AATGTTGGGCAGGTGCATCA 60.542 50.000 0.00 0.00 44.36 3.07
4133 5625 4.466370 TCATGTTCATCTTAGAACCGGAGT 59.534 41.667 9.46 0.00 45.62 3.85
4145 5637 0.886563 ACCGGAGTTCTACTTGACCG 59.113 55.000 9.46 0.00 34.18 4.79
4146 5638 0.458025 CCGGAGTTCTACTTGACCGC 60.458 60.000 0.00 0.00 33.38 5.68
4147 5639 0.526662 CGGAGTTCTACTTGACCGCT 59.473 55.000 0.00 0.00 28.63 5.52
4148 5640 1.467713 CGGAGTTCTACTTGACCGCTC 60.468 57.143 0.00 0.00 28.63 5.03
4158 5651 4.821589 GACCGCTCCCAGCCTTCG 62.822 72.222 0.00 0.00 38.18 3.79
4163 5656 2.348998 CTCCCAGCCTTCGTTGCT 59.651 61.111 0.00 0.00 40.41 3.91
4174 5667 3.190535 GCCTTCGTTGCTCTTTAAATGGA 59.809 43.478 0.00 0.00 0.00 3.41
4178 5671 5.309323 TCGTTGCTCTTTAAATGGATTGG 57.691 39.130 0.00 0.00 0.00 3.16
4231 5724 8.967664 TTACCTTTTGTGTAGTGATGTAAAGT 57.032 30.769 0.00 0.00 0.00 2.66
4240 5733 9.811995 TGTGTAGTGATGTAAAGTAATATGTCC 57.188 33.333 0.00 0.00 0.00 4.02
4241 5734 9.257651 GTGTAGTGATGTAAAGTAATATGTCCC 57.742 37.037 0.00 0.00 0.00 4.46
4242 5735 8.139350 TGTAGTGATGTAAAGTAATATGTCCCG 58.861 37.037 0.00 0.00 0.00 5.14
4243 5736 7.120923 AGTGATGTAAAGTAATATGTCCCGT 57.879 36.000 0.00 0.00 0.00 5.28
4244 5737 7.562135 AGTGATGTAAAGTAATATGTCCCGTT 58.438 34.615 0.00 0.00 0.00 4.44
4245 5738 8.698210 AGTGATGTAAAGTAATATGTCCCGTTA 58.302 33.333 0.00 0.00 0.00 3.18
4246 5739 9.485206 GTGATGTAAAGTAATATGTCCCGTTAT 57.515 33.333 0.00 0.00 0.00 1.89
4247 5740 9.701098 TGATGTAAAGTAATATGTCCCGTTATC 57.299 33.333 0.00 0.00 0.00 1.75
4248 5741 8.752766 ATGTAAAGTAATATGTCCCGTTATCG 57.247 34.615 0.00 0.00 0.00 2.92
4249 5742 7.939782 TGTAAAGTAATATGTCCCGTTATCGA 58.060 34.615 0.00 0.00 39.71 3.59
4250 5743 8.077991 TGTAAAGTAATATGTCCCGTTATCGAG 58.922 37.037 0.00 0.00 39.71 4.04
4251 5744 5.640189 AGTAATATGTCCCGTTATCGAGG 57.360 43.478 0.00 0.00 39.71 4.63
4252 5745 5.319453 AGTAATATGTCCCGTTATCGAGGA 58.681 41.667 0.00 0.00 39.71 3.71
4253 5746 4.516365 AATATGTCCCGTTATCGAGGAC 57.484 45.455 18.99 18.99 46.86 3.85
4254 5747 1.038280 ATGTCCCGTTATCGAGGACC 58.962 55.000 21.18 10.82 46.52 4.46
4255 5748 0.033796 TGTCCCGTTATCGAGGACCT 60.034 55.000 21.18 0.00 46.52 3.85
4256 5749 0.667453 GTCCCGTTATCGAGGACCTC 59.333 60.000 11.87 11.87 44.09 3.85
4257 5750 0.466922 TCCCGTTATCGAGGACCTCC 60.467 60.000 16.13 0.24 39.71 4.30
4282 5775 3.940229 AAAAATACGCCGTCTGGGA 57.060 47.368 0.00 0.00 38.47 4.37
4283 5776 1.734163 AAAAATACGCCGTCTGGGAG 58.266 50.000 0.00 0.00 42.10 4.30
4284 5777 0.743345 AAAATACGCCGTCTGGGAGC 60.743 55.000 0.00 0.00 39.59 4.70
4285 5778 1.614241 AAATACGCCGTCTGGGAGCT 61.614 55.000 0.00 0.00 39.59 4.09
4286 5779 1.614241 AATACGCCGTCTGGGAGCTT 61.614 55.000 0.00 0.00 39.59 3.74
4287 5780 1.614241 ATACGCCGTCTGGGAGCTTT 61.614 55.000 0.00 0.00 39.59 3.51
4288 5781 0.966875 TACGCCGTCTGGGAGCTTTA 60.967 55.000 0.00 0.00 39.59 1.85
4289 5782 1.810030 CGCCGTCTGGGAGCTTTAC 60.810 63.158 0.00 0.00 38.47 2.01
4290 5783 1.449778 GCCGTCTGGGAGCTTTACC 60.450 63.158 0.00 0.00 38.47 2.85
4291 5784 1.980052 CCGTCTGGGAGCTTTACCA 59.020 57.895 5.73 5.73 38.47 3.25
4292 5785 0.541863 CCGTCTGGGAGCTTTACCAT 59.458 55.000 6.24 0.00 38.47 3.55
4293 5786 1.656652 CGTCTGGGAGCTTTACCATG 58.343 55.000 6.24 0.00 35.93 3.66
4294 5787 1.207089 CGTCTGGGAGCTTTACCATGA 59.793 52.381 6.24 4.42 35.93 3.07
4295 5788 2.633488 GTCTGGGAGCTTTACCATGAC 58.367 52.381 6.24 10.96 35.93 3.06
4296 5789 2.237392 GTCTGGGAGCTTTACCATGACT 59.763 50.000 17.79 0.00 35.93 3.41
4297 5790 2.501723 TCTGGGAGCTTTACCATGACTC 59.498 50.000 6.24 0.00 35.93 3.36
4298 5791 2.237143 CTGGGAGCTTTACCATGACTCA 59.763 50.000 6.24 0.00 35.93 3.41
4299 5792 2.027192 TGGGAGCTTTACCATGACTCAC 60.027 50.000 0.00 0.00 0.00 3.51
4300 5793 2.237392 GGGAGCTTTACCATGACTCACT 59.763 50.000 0.00 0.00 0.00 3.41
4301 5794 3.451178 GGGAGCTTTACCATGACTCACTA 59.549 47.826 0.00 0.00 0.00 2.74
4302 5795 4.442192 GGGAGCTTTACCATGACTCACTAG 60.442 50.000 0.00 0.00 0.00 2.57
4303 5796 4.402793 GGAGCTTTACCATGACTCACTAGA 59.597 45.833 0.00 0.00 0.00 2.43
4304 5797 5.105310 GGAGCTTTACCATGACTCACTAGAA 60.105 44.000 0.00 0.00 0.00 2.10
4305 5798 6.360370 AGCTTTACCATGACTCACTAGAAA 57.640 37.500 0.00 0.00 0.00 2.52
4306 5799 6.769512 AGCTTTACCATGACTCACTAGAAAA 58.230 36.000 0.00 0.00 0.00 2.29
4307 5800 7.224297 AGCTTTACCATGACTCACTAGAAAAA 58.776 34.615 0.00 0.00 0.00 1.94
4308 5801 7.173390 AGCTTTACCATGACTCACTAGAAAAAC 59.827 37.037 0.00 0.00 0.00 2.43
4309 5802 7.041372 GCTTTACCATGACTCACTAGAAAAACA 60.041 37.037 0.00 0.00 0.00 2.83
4310 5803 7.724305 TTACCATGACTCACTAGAAAAACAC 57.276 36.000 0.00 0.00 0.00 3.32
4311 5804 5.063880 ACCATGACTCACTAGAAAAACACC 58.936 41.667 0.00 0.00 0.00 4.16
4312 5805 5.163195 ACCATGACTCACTAGAAAAACACCT 60.163 40.000 0.00 0.00 0.00 4.00
4313 5806 6.042781 ACCATGACTCACTAGAAAAACACCTA 59.957 38.462 0.00 0.00 0.00 3.08
4314 5807 6.934645 CCATGACTCACTAGAAAAACACCTAA 59.065 38.462 0.00 0.00 0.00 2.69
4315 5808 7.444183 CCATGACTCACTAGAAAAACACCTAAA 59.556 37.037 0.00 0.00 0.00 1.85
4316 5809 9.003658 CATGACTCACTAGAAAAACACCTAAAT 57.996 33.333 0.00 0.00 0.00 1.40
4317 5810 8.603242 TGACTCACTAGAAAAACACCTAAATC 57.397 34.615 0.00 0.00 0.00 2.17
4318 5811 8.208224 TGACTCACTAGAAAAACACCTAAATCA 58.792 33.333 0.00 0.00 0.00 2.57
4319 5812 8.608844 ACTCACTAGAAAAACACCTAAATCAG 57.391 34.615 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.449601 GCTTAAGCACGCCTAGGCA 60.450 57.895 32.47 10.00 40.21 4.75
118 139 0.521735 ATTTCTTGCCCGAGAAACGC 59.478 50.000 11.78 0.00 45.46 4.84
138 159 5.309282 GGTCTAATCCTCATCTGGGAGATTT 59.691 44.000 0.00 0.00 37.05 2.17
149 170 3.713764 CACAGGGAAGGTCTAATCCTCAT 59.286 47.826 0.00 0.00 36.74 2.90
164 185 2.366590 CGATGATGAATCCTCACAGGGA 59.633 50.000 0.00 0.00 39.95 4.20
182 203 0.249657 GCTGAATCCTCTTCGGCGAT 60.250 55.000 11.76 0.00 40.47 4.58
200 222 2.349886 GTCGATTTGTCATCAGAGTGGC 59.650 50.000 0.00 0.00 0.00 5.01
210 232 1.996898 CCGAAATCCGTCGATTTGTCA 59.003 47.619 4.62 0.00 46.48 3.58
222 244 2.565841 CTTGATCCCACTCCGAAATCC 58.434 52.381 0.00 0.00 0.00 3.01
227 249 1.860641 TAAGCTTGATCCCACTCCGA 58.139 50.000 9.86 0.00 0.00 4.55
231 253 3.557898 CGCCATATAAGCTTGATCCCACT 60.558 47.826 9.86 0.00 0.00 4.00
233 255 2.637382 TCGCCATATAAGCTTGATCCCA 59.363 45.455 9.86 0.00 0.00 4.37
240 262 5.049129 GCTCAATTTCTCGCCATATAAGCTT 60.049 40.000 3.48 3.48 0.00 3.74
248 270 2.421424 GTGAAGCTCAATTTCTCGCCAT 59.579 45.455 0.00 0.00 0.00 4.40
284 306 0.254178 CTCTGCCCCTTGCTACACAT 59.746 55.000 0.00 0.00 42.00 3.21
315 349 0.523072 GTTGGTGCATGATGTCGCTT 59.477 50.000 0.00 0.00 0.00 4.68
334 369 0.035630 CACCTGGCCCTCTTTCTCTG 60.036 60.000 0.00 0.00 0.00 3.35
340 398 0.695803 CCTATCCACCTGGCCCTCTT 60.696 60.000 0.00 0.00 34.44 2.85
348 406 3.849951 ACGCCGCCTATCCACCTG 61.850 66.667 0.00 0.00 0.00 4.00
352 410 3.536917 CCTCACGCCGCCTATCCA 61.537 66.667 0.00 0.00 0.00 3.41
372 430 6.937436 AGTCGACAACAAAATCTAGGTTTT 57.063 33.333 19.50 7.94 0.00 2.43
386 444 2.096909 GTGTGTGTGCATAGTCGACAAC 60.097 50.000 19.50 8.20 0.00 3.32
396 454 2.669569 GCTCCCGTGTGTGTGCAT 60.670 61.111 0.00 0.00 0.00 3.96
400 458 2.561478 ATTAAAGCTCCCGTGTGTGT 57.439 45.000 0.00 0.00 0.00 3.72
418 479 6.022315 CAGGTCCATCTTCCTATTCTCCTAT 58.978 44.000 0.00 0.00 32.26 2.57
458 519 2.221906 ATAAGCTATACGGGCCGGCG 62.222 60.000 31.78 15.66 0.00 6.46
462 523 5.049612 GTGAAAGAAATAAGCTATACGGGCC 60.050 44.000 0.00 0.00 0.00 5.80
487 550 5.983720 CGTAATTAGGCATTAGCACTGTAGT 59.016 40.000 0.00 0.00 44.61 2.73
513 576 5.179368 ACTTATGCACGATTAGCGCAATTAT 59.821 36.000 11.47 0.00 41.66 1.28
519 582 3.734231 TCTAACTTATGCACGATTAGCGC 59.266 43.478 0.00 0.00 46.04 5.92
542 606 0.313987 GCCACCTACTTGCGCTTTTT 59.686 50.000 9.73 0.00 0.00 1.94
634 716 8.795842 ATTTAACCGGATATGTTTTAGTCACA 57.204 30.769 9.46 0.00 0.00 3.58
656 738 9.236006 ACTGCTTCAATCAAGTATGACTAATTT 57.764 29.630 0.00 0.00 38.69 1.82
774 856 8.542080 ACCATGATGAAAATAAAACATGTCCAT 58.458 29.630 0.00 0.00 35.04 3.41
775 857 7.905265 ACCATGATGAAAATAAAACATGTCCA 58.095 30.769 0.00 0.00 35.04 4.02
776 858 9.520204 CTACCATGATGAAAATAAAACATGTCC 57.480 33.333 0.00 0.00 35.04 4.02
786 868 9.904198 TGTGAAAGATCTACCATGATGAAAATA 57.096 29.630 0.00 0.00 0.00 1.40
787 869 8.680903 GTGTGAAAGATCTACCATGATGAAAAT 58.319 33.333 0.00 0.00 0.00 1.82
792 874 6.596888 ACTTGTGTGAAAGATCTACCATGATG 59.403 38.462 0.00 0.00 0.00 3.07
793 875 6.715280 ACTTGTGTGAAAGATCTACCATGAT 58.285 36.000 0.00 0.00 0.00 2.45
809 891 2.425312 TGGCCTTGTACAAACTTGTGTG 59.575 45.455 10.03 0.00 42.31 3.82
810 892 2.687935 CTGGCCTTGTACAAACTTGTGT 59.312 45.455 10.03 0.00 42.31 3.72
811 893 2.948979 TCTGGCCTTGTACAAACTTGTG 59.051 45.455 10.03 0.00 42.31 3.33
812 894 3.214328 CTCTGGCCTTGTACAAACTTGT 58.786 45.455 10.03 0.07 44.86 3.16
813 895 2.554032 CCTCTGGCCTTGTACAAACTTG 59.446 50.000 10.03 0.00 0.00 3.16
814 896 2.863809 CCTCTGGCCTTGTACAAACTT 58.136 47.619 10.03 0.00 0.00 2.66
815 897 1.545651 GCCTCTGGCCTTGTACAAACT 60.546 52.381 10.03 0.00 44.06 2.66
816 898 0.881796 GCCTCTGGCCTTGTACAAAC 59.118 55.000 10.03 4.80 44.06 2.93
837 2069 1.660333 GCTTTGCTTGTTCGAGAACGG 60.660 52.381 10.86 7.65 43.94 4.44
888 2128 5.244626 ACTCGTTTAGTCAGCTAGGGTTTTA 59.755 40.000 0.00 0.00 30.33 1.52
923 2163 2.204306 AGGAGGAAGGGTTGGGGG 60.204 66.667 0.00 0.00 0.00 5.40
928 2168 1.008571 GGTAGAGGAGGAGGAAGGGTT 59.991 57.143 0.00 0.00 0.00 4.11
930 2170 0.637195 TGGTAGAGGAGGAGGAAGGG 59.363 60.000 0.00 0.00 0.00 3.95
1059 2309 1.454295 GGACGAGGAGGAGGAGGAC 60.454 68.421 0.00 0.00 0.00 3.85
1062 2312 3.213402 GCGGACGAGGAGGAGGAG 61.213 72.222 0.00 0.00 0.00 3.69
1294 2546 3.303132 GGCTACAGTAAAAATCGCATCGG 60.303 47.826 0.00 0.00 0.00 4.18
1384 2636 2.352225 GCAACCTGTTCACACAACACAA 60.352 45.455 0.00 0.00 30.36 3.33
1436 2691 3.923864 ACCTTCTGGTGCGACGCA 61.924 61.111 20.50 20.50 46.51 5.24
1547 2802 4.717233 TGCACCAACCAATCATAATGTC 57.283 40.909 0.00 0.00 0.00 3.06
1634 2892 6.313658 TCATTTGATATGTCTCACAAGTTCCG 59.686 38.462 0.00 0.00 0.00 4.30
1683 2941 8.081633 CAGGTGCTATCAAACAAACTCATAAAA 58.918 33.333 0.00 0.00 0.00 1.52
1788 3049 9.769093 AATCGTAAATTTGCACTAACATAGAAC 57.231 29.630 7.07 0.00 0.00 3.01
1799 3060 5.918011 TCTGGAAACAATCGTAAATTTGCAC 59.082 36.000 7.07 0.00 42.06 4.57
1815 3076 7.484140 AGAAAAACTCAAGTCAATCTGGAAAC 58.516 34.615 0.00 0.00 0.00 2.78
1819 3080 7.975616 TCAAAAGAAAAACTCAAGTCAATCTGG 59.024 33.333 0.00 0.00 0.00 3.86
1869 3130 6.553953 AATACATGGGCCGTCATATGTATA 57.446 37.500 20.52 3.65 42.66 1.47
1870 3131 5.435686 AATACATGGGCCGTCATATGTAT 57.564 39.130 16.59 16.59 44.33 2.29
1920 3181 6.515272 AACATTTCATATGACTGGACAACC 57.485 37.500 4.48 0.00 0.00 3.77
1921 3182 8.677300 ACATAACATTTCATATGACTGGACAAC 58.323 33.333 4.48 0.00 34.38 3.32
2061 3322 6.428159 TGAAAGTAAATCTCTCCTCTTGCAAC 59.572 38.462 0.00 0.00 0.00 4.17
2110 3371 3.005791 AGCAAGGTGGAGTATTTGTTTGC 59.994 43.478 0.00 0.00 39.79 3.68
2156 3417 0.037303 CCAGTGGAGAACCTGCATGT 59.963 55.000 1.68 0.00 33.78 3.21
2422 3683 7.120285 CCAGATCAACAGAGTCAATTTACATGT 59.880 37.037 2.69 2.69 0.00 3.21
2423 3684 7.120285 ACCAGATCAACAGAGTCAATTTACATG 59.880 37.037 0.00 0.00 0.00 3.21
2424 3685 7.170965 ACCAGATCAACAGAGTCAATTTACAT 58.829 34.615 0.00 0.00 0.00 2.29
2425 3686 6.533730 ACCAGATCAACAGAGTCAATTTACA 58.466 36.000 0.00 0.00 0.00 2.41
2426 3687 7.201565 GCTACCAGATCAACAGAGTCAATTTAC 60.202 40.741 0.00 0.00 0.00 2.01
2427 3688 6.818644 GCTACCAGATCAACAGAGTCAATTTA 59.181 38.462 0.00 0.00 0.00 1.40
2428 3689 5.645497 GCTACCAGATCAACAGAGTCAATTT 59.355 40.000 0.00 0.00 0.00 1.82
2429 3690 5.046014 AGCTACCAGATCAACAGAGTCAATT 60.046 40.000 0.00 0.00 0.00 2.32
2431 3692 3.834813 AGCTACCAGATCAACAGAGTCAA 59.165 43.478 0.00 0.00 0.00 3.18
2556 3948 4.646492 ACATCTTGTCAGGCTTTTGTTTCT 59.354 37.500 0.00 0.00 0.00 2.52
2557 3949 4.936891 ACATCTTGTCAGGCTTTTGTTTC 58.063 39.130 0.00 0.00 0.00 2.78
2558 3950 5.105392 TGAACATCTTGTCAGGCTTTTGTTT 60.105 36.000 0.00 0.00 0.00 2.83
2566 3958 5.412594 TGAGTTATTGAACATCTTGTCAGGC 59.587 40.000 0.00 0.00 38.10 4.85
2572 3964 6.094464 TGGCAGATGAGTTATTGAACATCTTG 59.906 38.462 0.00 0.00 44.30 3.02
2573 3965 6.182627 TGGCAGATGAGTTATTGAACATCTT 58.817 36.000 0.00 0.00 44.30 2.40
2577 3969 4.910195 ACTGGCAGATGAGTTATTGAACA 58.090 39.130 23.66 0.00 38.10 3.18
2589 3981 4.613622 CGGTTTCAACTTTACTGGCAGATG 60.614 45.833 23.66 10.05 0.00 2.90
2590 3982 3.502211 CGGTTTCAACTTTACTGGCAGAT 59.498 43.478 23.66 8.18 0.00 2.90
2603 3995 3.621715 ACACAGAAGAGTTCGGTTTCAAC 59.378 43.478 0.00 0.00 35.91 3.18
2610 4002 2.936498 ACACAAACACAGAAGAGTTCGG 59.064 45.455 0.00 0.00 34.02 4.30
2611 4003 5.712217 TTACACAAACACAGAAGAGTTCG 57.288 39.130 0.00 0.00 34.02 3.95
2624 4029 7.378728 GCCAGTCTCAACTATTTTTACACAAAC 59.621 37.037 0.00 0.00 33.25 2.93
2641 4046 4.365514 TCCACTAAAATTGCCAGTCTCA 57.634 40.909 0.00 0.00 0.00 3.27
2669 4074 8.839310 TGAATTGTTTTCTTCCAAGAACAAAA 57.161 26.923 9.54 2.97 44.18 2.44
2722 4128 9.113838 ACTTTCAATAAGCATTCCACATACTAG 57.886 33.333 0.00 0.00 0.00 2.57
2729 4135 8.462016 ACAGAATACTTTCAATAAGCATTCCAC 58.538 33.333 6.78 0.00 34.08 4.02
2813 4219 5.299028 TGTGTCAACAGCAAGAATAACATGT 59.701 36.000 0.00 0.00 0.00 3.21
2814 4220 5.761003 TGTGTCAACAGCAAGAATAACATG 58.239 37.500 0.00 0.00 0.00 3.21
2815 4221 6.005583 CTGTGTCAACAGCAAGAATAACAT 57.994 37.500 0.00 0.00 46.98 2.71
2879 4291 4.934797 AGACTCCATTCCTTCCAAATCA 57.065 40.909 0.00 0.00 0.00 2.57
2960 4372 2.226437 AGTGGCAGCACAATTTCTTACG 59.774 45.455 0.00 0.00 0.00 3.18
2973 4385 2.009774 ACATGAACGATAAGTGGCAGC 58.990 47.619 0.00 0.00 0.00 5.25
2983 4395 7.277981 GGTCAAGATACAAAGTACATGAACGAT 59.722 37.037 0.00 0.00 0.00 3.73
3208 4623 2.769663 AGATATGGTCAACGGTTAGCCA 59.230 45.455 14.97 14.97 34.09 4.75
3221 4636 2.025981 TGCAACAGCAAGGAGATATGGT 60.026 45.455 0.00 0.00 34.85 3.55
3228 4643 0.535780 TGTCCTGCAACAGCAAGGAG 60.536 55.000 8.28 0.00 37.91 3.69
3234 4649 1.668047 GCAAGATTGTCCTGCAACAGC 60.668 52.381 0.00 0.00 40.28 4.40
3336 4751 2.139917 GCTACACAAACGACACATGGA 58.860 47.619 0.00 0.00 0.00 3.41
3337 4752 2.143122 AGCTACACAAACGACACATGG 58.857 47.619 0.00 0.00 0.00 3.66
3345 4760 2.223377 GGAGTTGGAAGCTACACAAACG 59.777 50.000 0.00 0.00 0.00 3.60
3351 4766 1.340017 GGCATGGAGTTGGAAGCTACA 60.340 52.381 0.00 0.00 0.00 2.74
3358 4773 1.296392 CAGACGGCATGGAGTTGGA 59.704 57.895 0.00 0.00 0.00 3.53
3396 4819 7.650903 TGACAACATATTCTGATCTCTCATTCG 59.349 37.037 0.00 0.00 0.00 3.34
3476 4899 4.397417 AGTGCAAACATTAGGATCTCAAGC 59.603 41.667 0.00 0.00 0.00 4.01
3534 4957 6.366332 CAGCCAGAAACAAAGTACTAGTACTG 59.634 42.308 31.26 23.44 44.96 2.74
3536 4959 5.638234 CCAGCCAGAAACAAAGTACTAGTAC 59.362 44.000 23.03 23.03 36.35 2.73
3537 4960 5.541101 TCCAGCCAGAAACAAAGTACTAGTA 59.459 40.000 0.00 0.00 0.00 1.82
3538 4961 4.347000 TCCAGCCAGAAACAAAGTACTAGT 59.653 41.667 0.00 0.00 0.00 2.57
3539 4962 4.894784 TCCAGCCAGAAACAAAGTACTAG 58.105 43.478 0.00 0.00 0.00 2.57
3560 4983 9.277783 AGACAACTATCAGGCATTACAAATATC 57.722 33.333 0.00 0.00 0.00 1.63
3580 5003 3.434984 GCATTCACTCTTCCTCAGACAAC 59.565 47.826 0.00 0.00 0.00 3.32
3586 5009 1.339438 GCCAGCATTCACTCTTCCTCA 60.339 52.381 0.00 0.00 0.00 3.86
3593 5016 1.160137 AACGAAGCCAGCATTCACTC 58.840 50.000 0.00 0.00 0.00 3.51
3609 5032 3.506067 ACTAAATGGGAGCCAAGAAAACG 59.494 43.478 0.00 0.00 36.95 3.60
3618 5042 3.198853 AGTTCTCTGACTAAATGGGAGCC 59.801 47.826 0.00 0.00 0.00 4.70
3625 5049 5.690464 ATCCAGCAGTTCTCTGACTAAAT 57.310 39.130 0.00 0.00 43.76 1.40
3705 5130 6.491714 TTGTTTCAAGGGGAAAATGAATGA 57.508 33.333 0.00 0.00 46.53 2.57
3706 5131 7.565323 TTTTGTTTCAAGGGGAAAATGAATG 57.435 32.000 0.00 0.00 46.53 2.67
3741 5166 6.687604 TGACATACACTCTTCAATTCTTCGA 58.312 36.000 0.00 0.00 0.00 3.71
3742 5167 6.951256 TGACATACACTCTTCAATTCTTCG 57.049 37.500 0.00 0.00 0.00 3.79
3745 5170 9.950496 AGTATTTGACATACACTCTTCAATTCT 57.050 29.630 0.00 0.00 0.00 2.40
3748 5173 9.167311 GGAAGTATTTGACATACACTCTTCAAT 57.833 33.333 0.00 0.00 33.02 2.57
3749 5174 8.375506 AGGAAGTATTTGACATACACTCTTCAA 58.624 33.333 0.00 0.00 33.02 2.69
3836 5288 3.181482 CCTCAGCTCATCTTCATGTACGT 60.181 47.826 0.00 0.00 0.00 3.57
3853 5305 2.757099 GGGCATGGCAACCCTCAG 60.757 66.667 22.06 0.00 43.36 3.35
3858 5310 4.424711 TCGGAGGGCATGGCAACC 62.425 66.667 22.06 20.29 0.00 3.77
3860 5312 4.424711 GGTCGGAGGGCATGGCAA 62.425 66.667 22.06 0.00 0.00 4.52
3862 5314 4.195334 ATGGTCGGAGGGCATGGC 62.195 66.667 11.56 11.56 0.00 4.40
3863 5315 2.060567 ATCATGGTCGGAGGGCATGG 62.061 60.000 0.00 0.00 0.00 3.66
3864 5316 0.604780 GATCATGGTCGGAGGGCATG 60.605 60.000 0.00 0.00 0.00 4.06
3865 5317 1.757306 GATCATGGTCGGAGGGCAT 59.243 57.895 0.00 0.00 0.00 4.40
3866 5318 2.443394 GGATCATGGTCGGAGGGCA 61.443 63.158 0.00 0.00 0.00 5.36
3867 5319 2.388890 CTGGATCATGGTCGGAGGGC 62.389 65.000 0.00 0.00 0.00 5.19
3868 5320 1.750930 CTGGATCATGGTCGGAGGG 59.249 63.158 0.00 0.00 0.00 4.30
3869 5321 1.070445 GCTGGATCATGGTCGGAGG 59.930 63.158 0.00 0.00 0.00 4.30
3871 5323 2.796193 CCGCTGGATCATGGTCGGA 61.796 63.158 0.00 0.00 39.23 4.55
3872 5324 2.280389 CCGCTGGATCATGGTCGG 60.280 66.667 0.00 0.00 0.00 4.79
3873 5325 2.969238 GCCGCTGGATCATGGTCG 60.969 66.667 0.00 0.00 0.00 4.79
3874 5326 1.890979 CTGCCGCTGGATCATGGTC 60.891 63.158 0.00 0.00 0.00 4.02
3876 5328 1.597302 CTCTGCCGCTGGATCATGG 60.597 63.158 0.00 0.00 0.00 3.66
3877 5329 0.600518 CTCTCTGCCGCTGGATCATG 60.601 60.000 0.00 0.00 0.00 3.07
3890 5382 5.192327 AGTTTTGGTCAAATTGCTCTCTG 57.808 39.130 0.00 0.00 0.00 3.35
3891 5383 5.859205 AAGTTTTGGTCAAATTGCTCTCT 57.141 34.783 0.00 0.00 0.00 3.10
3919 5411 8.507249 AGACTATTACAGATTTGACTGCAAAAC 58.493 33.333 0.00 0.00 46.19 2.43
3922 5414 6.092670 GCAGACTATTACAGATTTGACTGCAA 59.907 38.462 0.00 0.00 43.87 4.08
3923 5415 5.582269 GCAGACTATTACAGATTTGACTGCA 59.418 40.000 0.00 0.00 43.87 4.41
3925 5417 5.525378 GGGCAGACTATTACAGATTTGACTG 59.475 44.000 0.00 0.00 42.78 3.51
3926 5418 5.396884 GGGGCAGACTATTACAGATTTGACT 60.397 44.000 0.00 0.00 0.00 3.41
3928 5420 4.473196 TGGGGCAGACTATTACAGATTTGA 59.527 41.667 0.00 0.00 0.00 2.69
3929 5421 4.780815 TGGGGCAGACTATTACAGATTTG 58.219 43.478 0.00 0.00 0.00 2.32
3930 5422 5.653255 ATGGGGCAGACTATTACAGATTT 57.347 39.130 0.00 0.00 0.00 2.17
3954 5446 4.021280 TGACCGTGGCTAACTACATAAACA 60.021 41.667 0.00 0.00 0.00 2.83
3955 5447 4.497300 TGACCGTGGCTAACTACATAAAC 58.503 43.478 0.00 0.00 0.00 2.01
3971 5463 1.598130 GTGCTCCAAGCTTGACCGT 60.598 57.895 28.05 0.00 42.97 4.83
3972 5464 0.886490 AAGTGCTCCAAGCTTGACCG 60.886 55.000 28.05 15.30 42.97 4.79
4013 5505 3.146066 TGACCAGCCTTACATGTTTGTC 58.854 45.455 2.30 0.00 37.28 3.18
4016 5508 4.032960 TGATGACCAGCCTTACATGTTT 57.967 40.909 2.30 0.00 0.00 2.83
4026 5518 0.534652 GAGGCTCATGATGACCAGCC 60.535 60.000 14.35 14.35 36.00 4.85
4031 5523 0.879400 CGCAGGAGGCTCATGATGAC 60.879 60.000 31.24 13.19 41.67 3.06
4042 5534 1.002366 CAAACGAAGATCGCAGGAGG 58.998 55.000 0.00 0.00 45.12 4.30
4047 5539 2.128821 TCGAAACAAACGAAGATCGCA 58.871 42.857 0.00 0.00 45.12 5.10
4064 5556 4.157656 CCTGCCCAACATTAAAAAGATCGA 59.842 41.667 0.00 0.00 0.00 3.59
4065 5557 4.082245 ACCTGCCCAACATTAAAAAGATCG 60.082 41.667 0.00 0.00 0.00 3.69
4067 5559 4.563374 GCACCTGCCCAACATTAAAAAGAT 60.563 41.667 0.00 0.00 34.31 2.40
4074 5566 1.272369 TGATGCACCTGCCCAACATTA 60.272 47.619 0.00 0.00 41.18 1.90
4075 5567 0.542467 TGATGCACCTGCCCAACATT 60.542 50.000 0.00 0.00 41.18 2.71
4076 5568 0.324923 ATGATGCACCTGCCCAACAT 60.325 50.000 0.00 0.00 41.18 2.71
4080 5572 2.276409 GGATGATGCACCTGCCCA 59.724 61.111 0.00 0.00 41.18 5.36
4108 5600 5.359756 TCCGGTTCTAAGATGAACATGATG 58.640 41.667 0.00 0.00 45.74 3.07
4133 5625 0.895530 CTGGGAGCGGTCAAGTAGAA 59.104 55.000 17.59 0.00 0.00 2.10
4144 5636 3.121030 CAACGAAGGCTGGGAGCG 61.121 66.667 0.00 0.00 43.62 5.03
4145 5637 3.435186 GCAACGAAGGCTGGGAGC 61.435 66.667 0.00 0.00 41.46 4.70
4146 5638 1.743252 GAGCAACGAAGGCTGGGAG 60.743 63.158 5.07 0.00 42.78 4.30
4147 5639 1.768684 AAGAGCAACGAAGGCTGGGA 61.769 55.000 5.07 0.00 42.78 4.37
4148 5640 0.890996 AAAGAGCAACGAAGGCTGGG 60.891 55.000 5.07 0.00 42.78 4.45
4158 5651 7.375053 TGTTACCAATCCATTTAAAGAGCAAC 58.625 34.615 0.00 0.00 0.00 4.17
4159 5652 7.531857 TGTTACCAATCCATTTAAAGAGCAA 57.468 32.000 0.00 0.00 0.00 3.91
4163 5656 7.716799 AGCATGTTACCAATCCATTTAAAGA 57.283 32.000 0.00 0.00 0.00 2.52
4208 5701 8.967664 TTACTTTACATCACTACACAAAAGGT 57.032 30.769 0.00 0.00 0.00 3.50
4230 5723 5.633830 TCCTCGATAACGGGACATATTAC 57.366 43.478 0.00 0.00 43.41 1.89
4237 5730 4.981263 AGGAGGTCCTCGATAACGGGAC 62.981 59.091 18.38 18.38 44.77 4.46
4238 5731 0.466922 GGAGGTCCTCGATAACGGGA 60.467 60.000 12.91 0.00 43.41 5.14
4239 5732 0.467659 AGGAGGTCCTCGATAACGGG 60.468 60.000 12.91 0.00 44.77 5.28
4240 5733 3.112965 AGGAGGTCCTCGATAACGG 57.887 57.895 12.91 0.00 44.77 4.44
4264 5757 1.734163 CTCCCAGACGGCGTATTTTT 58.266 50.000 14.74 0.00 0.00 1.94
4265 5758 0.743345 GCTCCCAGACGGCGTATTTT 60.743 55.000 14.74 0.00 0.00 1.82
4266 5759 1.153429 GCTCCCAGACGGCGTATTT 60.153 57.895 14.74 0.00 0.00 1.40
4267 5760 1.614241 AAGCTCCCAGACGGCGTATT 61.614 55.000 14.74 0.48 0.00 1.89
4268 5761 1.614241 AAAGCTCCCAGACGGCGTAT 61.614 55.000 14.74 7.06 0.00 3.06
4269 5762 0.966875 TAAAGCTCCCAGACGGCGTA 60.967 55.000 14.74 0.00 0.00 4.42
4270 5763 2.280552 TAAAGCTCCCAGACGGCGT 61.281 57.895 14.65 14.65 0.00 5.68
4271 5764 1.810030 GTAAAGCTCCCAGACGGCG 60.810 63.158 4.80 4.80 0.00 6.46
4272 5765 1.449778 GGTAAAGCTCCCAGACGGC 60.450 63.158 0.00 0.00 0.00 5.68
4273 5766 0.541863 ATGGTAAAGCTCCCAGACGG 59.458 55.000 6.00 0.00 33.39 4.79
4274 5767 1.207089 TCATGGTAAAGCTCCCAGACG 59.793 52.381 6.00 0.00 33.39 4.18
4275 5768 2.237392 AGTCATGGTAAAGCTCCCAGAC 59.763 50.000 14.66 14.66 33.39 3.51
4276 5769 2.501723 GAGTCATGGTAAAGCTCCCAGA 59.498 50.000 6.00 2.09 33.39 3.86
4277 5770 2.237143 TGAGTCATGGTAAAGCTCCCAG 59.763 50.000 6.00 0.17 33.39 4.45
4278 5771 2.027192 GTGAGTCATGGTAAAGCTCCCA 60.027 50.000 0.00 2.55 34.66 4.37
4279 5772 2.237392 AGTGAGTCATGGTAAAGCTCCC 59.763 50.000 0.00 0.00 0.00 4.30
4280 5773 3.618690 AGTGAGTCATGGTAAAGCTCC 57.381 47.619 0.00 0.00 0.00 4.70
4281 5774 5.584253 TCTAGTGAGTCATGGTAAAGCTC 57.416 43.478 0.00 0.00 0.00 4.09
4282 5775 6.360370 TTTCTAGTGAGTCATGGTAAAGCT 57.640 37.500 0.00 0.00 0.00 3.74
4283 5776 7.041372 TGTTTTTCTAGTGAGTCATGGTAAAGC 60.041 37.037 0.00 0.25 0.00 3.51
4284 5777 8.283291 GTGTTTTTCTAGTGAGTCATGGTAAAG 58.717 37.037 0.00 0.00 0.00 1.85
4285 5778 7.227910 GGTGTTTTTCTAGTGAGTCATGGTAAA 59.772 37.037 0.00 0.00 0.00 2.01
4286 5779 6.708949 GGTGTTTTTCTAGTGAGTCATGGTAA 59.291 38.462 0.00 0.00 0.00 2.85
4287 5780 6.042781 AGGTGTTTTTCTAGTGAGTCATGGTA 59.957 38.462 0.00 0.00 0.00 3.25
4288 5781 5.063880 GGTGTTTTTCTAGTGAGTCATGGT 58.936 41.667 0.00 0.00 0.00 3.55
4289 5782 5.308825 AGGTGTTTTTCTAGTGAGTCATGG 58.691 41.667 0.00 0.00 0.00 3.66
4290 5783 7.962964 TTAGGTGTTTTTCTAGTGAGTCATG 57.037 36.000 0.00 0.00 0.00 3.07
4291 5784 9.220767 GATTTAGGTGTTTTTCTAGTGAGTCAT 57.779 33.333 0.00 0.00 0.00 3.06
4292 5785 8.208224 TGATTTAGGTGTTTTTCTAGTGAGTCA 58.792 33.333 0.00 0.00 0.00 3.41
4293 5786 8.603242 TGATTTAGGTGTTTTTCTAGTGAGTC 57.397 34.615 0.00 0.00 0.00 3.36
4294 5787 7.661847 CCTGATTTAGGTGTTTTTCTAGTGAGT 59.338 37.037 0.00 0.00 42.00 3.41
4295 5788 8.034058 CCTGATTTAGGTGTTTTTCTAGTGAG 57.966 38.462 0.00 0.00 42.00 3.51
4296 5789 7.979444 CCTGATTTAGGTGTTTTTCTAGTGA 57.021 36.000 0.00 0.00 42.00 3.41


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

AutoCloner maintained by Alex Coulton.