Multiple sequence alignment - TraesCS4B01G137900

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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 TraesCS4B01G137900 chr4B 100.000 4019 0 0 1 4019 181696374 181692356 0.000000e+00 7422.0
1 TraesCS4B01G137900 chr4B 100.000 156 0 0 4345 4500 181692030 181691875 5.700000e-74 289.0
2 TraesCS4B01G137900 chr4B 89.796 49 2 1 3431 3479 453766782 453766737 4.860000e-05 60.2
3 TraesCS4B01G137900 chr4A 91.657 3476 177 54 1 3426 449893260 449889848 0.000000e+00 4708.0
4 TraesCS4B01G137900 chr4A 80.357 392 25 23 3515 3881 449889822 449889458 2.690000e-62 250.0
5 TraesCS4B01G137900 chr4A 98.450 129 2 0 4359 4487 449820276 449820148 1.260000e-55 228.0
6 TraesCS4B01G137900 chr4A 92.222 90 7 0 3916 4005 449889460 449889371 1.310000e-25 128.0
7 TraesCS4B01G137900 chr4A 89.796 49 2 1 3431 3479 96309602 96309647 4.860000e-05 60.2
8 TraesCS4B01G137900 chr4D 95.402 1979 69 9 824 2794 119414743 119412779 0.000000e+00 3131.0
9 TraesCS4B01G137900 chr4D 95.272 698 30 3 2787 3481 119412702 119412005 0.000000e+00 1103.0
10 TraesCS4B01G137900 chr4D 92.264 530 18 5 3502 4019 119411961 119411443 0.000000e+00 730.0
11 TraesCS4B01G137900 chr4D 94.524 420 16 3 1 418 119415523 119415109 3.800000e-180 641.0
12 TraesCS4B01G137900 chr4D 98.639 147 2 0 4354 4500 119411331 119411185 1.240000e-65 261.0
13 TraesCS4B01G137900 chr1D 88.462 52 3 2 3428 3479 130610028 130610076 4.860000e-05 60.2
14 TraesCS4B01G137900 chr1B 88.462 52 3 2 3428 3479 207268206 207268254 4.860000e-05 60.2
15 TraesCS4B01G137900 chr1B 100.000 29 0 0 3451 3479 397429448 397429420 2.000000e-03 54.7
16 TraesCS4B01G137900 chr1A 88.462 52 3 2 3428 3479 189960945 189960993 4.860000e-05 60.2
17 TraesCS4B01G137900 chr1A 100.000 29 0 0 3451 3479 368812581 368812553 2.000000e-03 54.7
18 TraesCS4B01G137900 chr6B 96.970 33 0 1 3448 3479 227650150 227650182 2.000000e-03 54.7


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 TraesCS4B01G137900 chr4B 181691875 181696374 4499 True 3855.500000 7422 100.000000 1 4500 2 chr4B.!!$R2 4499
1 TraesCS4B01G137900 chr4A 449889371 449893260 3889 True 1695.333333 4708 88.078667 1 4005 3 chr4A.!!$R2 4004
2 TraesCS4B01G137900 chr4D 119411185 119415523 4338 True 1173.200000 3131 95.220200 1 4500 5 chr4D.!!$R1 4499

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
968 992 0.036765 CTGCATGCCAAGTTGCCAAT 60.037 50.0 16.68 0.0 38.08 3.16 F
2306 2359 0.108186 TATCAGTGCAAGGACGGCAG 60.108 55.0 0.00 0.0 42.85 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2654 2708 0.322008 CCAAGCTCCTCAGGTTCACC 60.322 60.0 0.0 0.0 38.33 4.02 R
3804 4015 0.107456 AGAGCTGTGTGTTGGTGGAG 59.893 55.0 0.0 0.0 0.00 3.86 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
70 72 2.018355 TGAACTAGTGGTGGCTGGTA 57.982 50.000 0.00 0.00 29.89 3.25
77 79 1.774856 AGTGGTGGCTGGTAAGAAAGT 59.225 47.619 0.00 0.00 0.00 2.66
103 105 0.948623 GCGCACACACCAGACATGTA 60.949 55.000 0.30 0.00 0.00 2.29
104 106 0.790207 CGCACACACCAGACATGTAC 59.210 55.000 0.00 0.00 0.00 2.90
105 107 1.605457 CGCACACACCAGACATGTACT 60.605 52.381 0.00 0.00 0.00 2.73
106 108 1.800586 GCACACACCAGACATGTACTG 59.199 52.381 14.68 14.68 35.43 2.74
107 109 2.806745 GCACACACCAGACATGTACTGT 60.807 50.000 18.09 7.59 42.15 3.55
146 149 9.659830 AAAAGCAAAGTATGTCTTAAAGTTACG 57.340 29.630 0.00 0.00 35.02 3.18
412 417 2.032054 TCAATGCTTTATACGCTGCTGC 59.968 45.455 5.34 5.34 0.00 5.25
435 440 4.402474 CCTTGTCTTTCCACCTGTTTTTCT 59.598 41.667 0.00 0.00 0.00 2.52
440 445 2.435372 TCCACCTGTTTTTCTGCAGT 57.565 45.000 14.67 0.00 0.00 4.40
442 447 2.023673 CCACCTGTTTTTCTGCAGTCA 58.976 47.619 14.67 0.00 0.00 3.41
524 540 7.564793 TCAGATGCAAGTATACACCAAGTTAT 58.435 34.615 5.50 0.00 0.00 1.89
538 554 5.647658 CACCAAGTTATAGGAAATGACTGCA 59.352 40.000 0.00 0.00 0.00 4.41
539 555 6.319658 CACCAAGTTATAGGAAATGACTGCAT 59.680 38.462 0.00 0.00 35.92 3.96
540 556 6.319658 ACCAAGTTATAGGAAATGACTGCATG 59.680 38.462 0.00 0.00 34.26 4.06
541 557 6.543465 CCAAGTTATAGGAAATGACTGCATGA 59.457 38.462 0.00 0.00 34.26 3.07
542 558 7.230108 CCAAGTTATAGGAAATGACTGCATGAT 59.770 37.037 0.00 0.00 34.26 2.45
543 559 9.276590 CAAGTTATAGGAAATGACTGCATGATA 57.723 33.333 0.00 0.00 34.26 2.15
544 560 9.851686 AAGTTATAGGAAATGACTGCATGATAA 57.148 29.630 0.00 0.00 34.26 1.75
545 561 9.851686 AGTTATAGGAAATGACTGCATGATAAA 57.148 29.630 0.00 0.00 34.26 1.40
572 588 7.726033 AACTAGAGTCTTCATACACCAGAAT 57.274 36.000 0.00 0.00 0.00 2.40
573 589 7.341445 ACTAGAGTCTTCATACACCAGAATC 57.659 40.000 0.00 0.00 32.90 2.52
584 600 8.212317 TCATACACCAGAATCATACAAACATG 57.788 34.615 0.00 0.00 0.00 3.21
612 628 3.310501 GGGACGGTAATTACCATTTGACG 59.689 47.826 29.56 17.77 46.80 4.35
619 635 6.310956 CGGTAATTACCATTTGACGTGTAGAA 59.689 38.462 29.56 0.00 46.80 2.10
647 663 6.018751 GAGTAGATCTCGTATTGCAATGCAAA 60.019 38.462 25.06 11.29 41.46 3.68
687 706 8.127954 GTGTTTTCGGTTGGTTAAATAGTAACA 58.872 33.333 0.00 0.00 0.00 2.41
725 744 2.563179 GTGTCTCTGCTTTCTGGTCCTA 59.437 50.000 0.00 0.00 0.00 2.94
728 747 4.287067 TGTCTCTGCTTTCTGGTCCTATTT 59.713 41.667 0.00 0.00 0.00 1.40
736 755 5.422214 TTTCTGGTCCTATTTGTCCTCTC 57.578 43.478 0.00 0.00 0.00 3.20
737 756 4.061131 TCTGGTCCTATTTGTCCTCTCA 57.939 45.455 0.00 0.00 0.00 3.27
738 757 4.624913 TCTGGTCCTATTTGTCCTCTCAT 58.375 43.478 0.00 0.00 0.00 2.90
740 759 3.455910 TGGTCCTATTTGTCCTCTCATGG 59.544 47.826 0.00 0.00 0.00 3.66
742 761 2.439507 TCCTATTTGTCCTCTCATGGCC 59.560 50.000 0.00 0.00 0.00 5.36
743 762 2.173356 CCTATTTGTCCTCTCATGGCCA 59.827 50.000 8.56 8.56 0.00 5.36
747 766 1.288188 TGTCCTCTCATGGCCAATGA 58.712 50.000 10.96 13.41 43.24 2.57
768 787 0.179111 CGATTGGCCGCTCTCAACTA 60.179 55.000 0.00 0.00 0.00 2.24
777 796 1.090728 GCTCTCAACTAAAGCAGCCC 58.909 55.000 0.00 0.00 36.06 5.19
779 798 2.354259 CTCTCAACTAAAGCAGCCCAG 58.646 52.381 0.00 0.00 0.00 4.45
781 800 0.609131 TCAACTAAAGCAGCCCAGCC 60.609 55.000 0.00 0.00 34.23 4.85
782 801 0.610232 CAACTAAAGCAGCCCAGCCT 60.610 55.000 0.00 0.00 34.23 4.58
784 803 0.991920 ACTAAAGCAGCCCAGCCTAA 59.008 50.000 0.00 0.00 34.23 2.69
791 810 0.466124 CAGCCCAGCCTAACCTACTC 59.534 60.000 0.00 0.00 0.00 2.59
792 811 1.043673 AGCCCAGCCTAACCTACTCG 61.044 60.000 0.00 0.00 0.00 4.18
793 812 1.442148 CCCAGCCTAACCTACTCGC 59.558 63.158 0.00 0.00 0.00 5.03
794 813 1.327690 CCCAGCCTAACCTACTCGCA 61.328 60.000 0.00 0.00 0.00 5.10
795 814 0.753262 CCAGCCTAACCTACTCGCAT 59.247 55.000 0.00 0.00 0.00 4.73
797 816 2.364324 CCAGCCTAACCTACTCGCATTA 59.636 50.000 0.00 0.00 0.00 1.90
800 819 4.270325 CAGCCTAACCTACTCGCATTAAAC 59.730 45.833 0.00 0.00 0.00 2.01
809 828 3.825308 ACTCGCATTAAACACAGCAATG 58.175 40.909 0.00 0.00 33.69 2.82
968 992 0.036765 CTGCATGCCAAGTTGCCAAT 60.037 50.000 16.68 0.00 38.08 3.16
1058 1082 1.068333 CGCAACACAGCAATAAAGGCT 60.068 47.619 0.00 0.00 43.77 4.58
1059 1083 2.161410 CGCAACACAGCAATAAAGGCTA 59.839 45.455 0.00 0.00 40.23 3.93
1060 1084 3.728864 CGCAACACAGCAATAAAGGCTAG 60.729 47.826 0.00 0.00 40.23 3.42
1078 1102 5.952526 GCTAGTAGAACTCTAGGCTTAGG 57.047 47.826 0.00 0.00 36.40 2.69
1079 1103 4.216902 GCTAGTAGAACTCTAGGCTTAGGC 59.783 50.000 0.00 0.00 36.40 3.93
1080 1104 4.529716 AGTAGAACTCTAGGCTTAGGCT 57.470 45.455 13.95 13.95 42.39 4.58
1152 1176 2.074948 ATGGCGGCAGGATCTCCTT 61.075 57.895 19.29 0.00 46.09 3.36
1198 1231 3.429141 CCAAGAGCAGCAGCACCG 61.429 66.667 3.17 0.00 45.49 4.94
1225 1258 1.893919 AAGCTCCTTCGTCTCCAGCC 61.894 60.000 0.00 0.00 0.00 4.85
1427 1460 1.073025 AACACCGAGCTGGAATGCA 59.927 52.632 8.91 0.00 42.00 3.96
1429 1462 0.322816 ACACCGAGCTGGAATGCAAT 60.323 50.000 8.91 0.00 42.00 3.56
1522 1555 2.166254 CCATGTAAGTTGGGTTCCATGC 59.834 50.000 0.00 0.00 31.53 4.06
1579 1612 5.689383 TCTTCTTCCATTTCCTGAAAACG 57.311 39.130 0.00 0.00 33.56 3.60
1580 1613 3.915437 TCTTCCATTTCCTGAAAACGC 57.085 42.857 0.00 0.00 33.56 4.84
1585 1619 3.383185 TCCATTTCCTGAAAACGCAACTT 59.617 39.130 0.00 0.00 33.56 2.66
1590 1624 7.596995 CCATTTCCTGAAAACGCAACTTAATTA 59.403 33.333 0.00 0.00 33.56 1.40
1656 1699 3.931468 GAGATGTCCATGTTCACTCACAG 59.069 47.826 0.00 0.00 0.00 3.66
1755 1798 2.535574 GCAACGAAGCAACCAAAAAGAG 59.464 45.455 0.00 0.00 0.00 2.85
2044 2091 0.963962 CAGCACCTTGCCATGAAACT 59.036 50.000 0.00 0.00 46.52 2.66
2086 2133 7.869937 TGCTAGACATGATTTCTTACTAGATGC 59.130 37.037 0.00 0.00 0.00 3.91
2091 2142 9.481340 GACATGATTTCTTACTAGATGCATGTA 57.519 33.333 2.46 2.92 41.55 2.29
2281 2334 9.650539 CACAATTATATTTGGTTCCATTTGTCA 57.349 29.630 11.09 0.00 0.00 3.58
2306 2359 0.108186 TATCAGTGCAAGGACGGCAG 60.108 55.000 0.00 0.00 42.85 4.85
2310 2363 3.939939 TGCAAGGACGGCAGCTGA 61.940 61.111 20.43 0.00 36.11 4.26
2378 2432 2.887568 CTGATGAGACCGGCGTGC 60.888 66.667 6.01 0.00 0.00 5.34
2419 2473 0.326264 AGAGGAAAGCCGATGCACTT 59.674 50.000 0.00 0.00 41.13 3.16
2537 2591 5.010516 GCTACTCTGAGGAAGATATCAAGCA 59.989 44.000 9.85 0.00 33.29 3.91
2654 2708 4.767478 TGGAGAAGAGCATGAAGAGATTG 58.233 43.478 0.00 0.00 0.00 2.67
2671 2725 1.140312 TTGGTGAACCTGAGGAGCTT 58.860 50.000 4.99 0.00 36.82 3.74
2757 2811 7.380536 TGCTTCGAAGGTAGTCAGTTAATTAA 58.619 34.615 25.77 0.00 0.00 1.40
2769 2823 7.684670 AGTCAGTTAATTAATATGTGCGTGTG 58.315 34.615 0.31 0.00 0.00 3.82
2828 2965 6.899393 TTTGCATCAAACAGAGATTAACCT 57.101 33.333 0.00 0.00 0.00 3.50
2845 2982 2.661718 ACCTGTTGGGAATTGTTCGTT 58.338 42.857 0.00 0.00 38.76 3.85
2858 2995 7.413548 GGGAATTGTTCGTTTGTTTGAATTTGT 60.414 33.333 0.00 0.00 0.00 2.83
2869 3006 6.817765 TGTTTGAATTTGTAGATGAGGGTC 57.182 37.500 0.00 0.00 0.00 4.46
2959 3096 1.615384 GGGAATGAGGCTGCTCTTGTT 60.615 52.381 0.00 0.00 0.00 2.83
3068 3205 8.928733 TGCTCATTTTATTTGCTTGATTTCTTC 58.071 29.630 0.00 0.00 0.00 2.87
3184 3322 5.221891 AGATGAAACGAAATGATTGTCGG 57.778 39.130 12.03 0.00 41.56 4.79
3204 3342 5.518847 GTCGGTGAATGAGATGAAACGATTA 59.481 40.000 0.00 0.00 0.00 1.75
3261 3401 3.064820 CGTGGGTTTTGTATGGAGCATAC 59.935 47.826 0.00 0.00 44.74 2.39
3270 3410 4.608948 GTATGGAGCATACAGGCTAGTT 57.391 45.455 0.00 0.00 45.99 2.24
3271 3411 4.962155 GTATGGAGCATACAGGCTAGTTT 58.038 43.478 0.00 0.00 45.99 2.66
3438 3583 6.544931 ACTTTTTGTGTTCTTAAGTACTCCCC 59.455 38.462 12.72 0.94 0.00 4.81
3482 3655 7.760340 AGGACGTTTTTGCAGTTTAAATTTACA 59.240 29.630 0.00 0.00 0.00 2.41
3486 3659 9.015577 CGTTTTTGCAGTTTAAATTTACAGAGA 57.984 29.630 0.00 0.00 0.00 3.10
3528 3701 7.916128 TGAATGTAACGTTGTAACATTTTGG 57.084 32.000 22.32 0.00 42.35 3.28
3532 3705 3.994204 ACGTTGTAACATTTTGGGGAC 57.006 42.857 0.00 0.00 0.00 4.46
3590 3763 1.368850 GCACAAAGTCGACGGTTGC 60.369 57.895 25.60 20.69 0.00 4.17
3633 3806 3.254166 GTCCATGTGTTTGATGTTCTGCT 59.746 43.478 0.00 0.00 0.00 4.24
3653 3835 3.616379 GCTGCTAACAAACAAACAAGCAA 59.384 39.130 0.00 0.00 39.29 3.91
3786 3975 2.174319 GCTACAGCTTAGGCGCACC 61.174 63.158 10.83 0.00 44.37 5.01
3914 4125 2.820178 TGAAGCACTCCTCTATGTCCA 58.180 47.619 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 66 2.427506 CCACCTGACTTTCTTACCAGC 58.572 52.381 0.00 0.00 0.00 4.85
70 72 1.148273 TGCGCCACCTGACTTTCTT 59.852 52.632 4.18 0.00 0.00 2.52
171 175 5.412594 TCATGTTCAAGGCTCACTAACAATC 59.587 40.000 7.64 0.00 34.08 2.67
220 224 1.792301 CAGCACACCAGAATCTGCG 59.208 57.895 4.40 0.48 34.69 5.18
391 396 2.032054 GCAGCAGCGTATAAAGCATTGA 59.968 45.455 4.55 0.00 37.01 2.57
404 409 1.208614 GAAAGACAAGGCAGCAGCG 59.791 57.895 0.00 0.00 43.41 5.18
412 417 4.402474 AGAAAAACAGGTGGAAAGACAAGG 59.598 41.667 0.00 0.00 0.00 3.61
461 468 5.450965 GCATTGGTTCTTGTAATCCCATCTG 60.451 44.000 0.00 0.00 0.00 2.90
494 510 8.978874 TTGGTGTATACTTGCATCTGAATTAT 57.021 30.769 4.17 0.00 0.00 1.28
495 511 8.046708 ACTTGGTGTATACTTGCATCTGAATTA 58.953 33.333 4.17 0.00 0.00 1.40
496 512 6.886459 ACTTGGTGTATACTTGCATCTGAATT 59.114 34.615 4.17 0.00 0.00 2.17
497 513 6.418101 ACTTGGTGTATACTTGCATCTGAAT 58.582 36.000 4.17 0.00 0.00 2.57
498 514 5.804639 ACTTGGTGTATACTTGCATCTGAA 58.195 37.500 4.17 0.00 0.00 3.02
499 515 5.420725 ACTTGGTGTATACTTGCATCTGA 57.579 39.130 4.17 0.00 0.00 3.27
512 528 6.821665 GCAGTCATTTCCTATAACTTGGTGTA 59.178 38.462 0.00 0.00 0.00 2.90
513 529 5.648092 GCAGTCATTTCCTATAACTTGGTGT 59.352 40.000 0.00 0.00 0.00 4.16
532 548 9.757227 AGACTCTAGTTATTTTATCATGCAGTC 57.243 33.333 0.00 0.00 0.00 3.51
543 559 9.877178 CTGGTGTATGAAGACTCTAGTTATTTT 57.123 33.333 0.00 0.00 0.00 1.82
544 560 9.256228 TCTGGTGTATGAAGACTCTAGTTATTT 57.744 33.333 0.00 0.00 0.00 1.40
545 561 8.824756 TCTGGTGTATGAAGACTCTAGTTATT 57.175 34.615 0.00 0.00 0.00 1.40
554 570 7.423844 TGTATGATTCTGGTGTATGAAGACT 57.576 36.000 0.00 0.00 0.00 3.24
619 635 7.032580 GCATTGCAATACGAGATCTACTCTAT 58.967 38.462 12.53 0.00 42.92 1.98
736 755 3.951115 CAATCGGTCATTGGCCATG 57.049 52.632 6.09 7.61 38.67 3.66
742 761 2.114670 AGCGGCCAATCGGTCATTG 61.115 57.895 2.24 0.00 41.64 2.82
743 762 2.272146 AGCGGCCAATCGGTCATT 59.728 55.556 2.24 0.00 36.30 2.57
747 766 2.954684 TTGAGAGCGGCCAATCGGT 61.955 57.895 2.24 0.00 43.85 4.69
756 775 0.723981 GCTGCTTTAGTTGAGAGCGG 59.276 55.000 0.00 0.00 43.85 5.52
758 777 1.090728 GGGCTGCTTTAGTTGAGAGC 58.909 55.000 0.00 0.00 36.95 4.09
768 787 1.304464 GGTTAGGCTGGGCTGCTTT 60.304 57.895 6.93 0.00 0.00 3.51
777 796 2.604046 AATGCGAGTAGGTTAGGCTG 57.396 50.000 0.00 0.00 0.00 4.85
779 798 4.033702 GTGTTTAATGCGAGTAGGTTAGGC 59.966 45.833 0.00 0.00 0.00 3.93
781 800 5.220416 GCTGTGTTTAATGCGAGTAGGTTAG 60.220 44.000 0.00 0.00 0.00 2.34
782 801 4.628333 GCTGTGTTTAATGCGAGTAGGTTA 59.372 41.667 0.00 0.00 0.00 2.85
784 803 3.000727 GCTGTGTTTAATGCGAGTAGGT 58.999 45.455 0.00 0.00 0.00 3.08
791 810 3.173599 CCTCATTGCTGTGTTTAATGCG 58.826 45.455 0.00 0.00 33.10 4.73
792 811 4.178545 ACCTCATTGCTGTGTTTAATGC 57.821 40.909 0.00 0.00 33.10 3.56
793 812 5.771469 TGAACCTCATTGCTGTGTTTAATG 58.229 37.500 0.00 0.00 34.07 1.90
794 813 5.047802 CCTGAACCTCATTGCTGTGTTTAAT 60.048 40.000 0.00 0.00 0.00 1.40
795 814 4.278170 CCTGAACCTCATTGCTGTGTTTAA 59.722 41.667 0.00 0.00 0.00 1.52
797 816 2.624838 CCTGAACCTCATTGCTGTGTTT 59.375 45.455 0.00 0.00 0.00 2.83
800 819 0.524862 GCCTGAACCTCATTGCTGTG 59.475 55.000 0.00 0.00 0.00 3.66
809 828 2.045536 CCTGCCTGCCTGAACCTC 60.046 66.667 0.00 0.00 0.00 3.85
924 948 1.496857 TGGGTTGTGGAACTGGAATCA 59.503 47.619 0.00 0.00 38.04 2.57
927 951 0.626382 TGTGGGTTGTGGAACTGGAA 59.374 50.000 0.00 0.00 38.04 3.53
928 952 0.850100 ATGTGGGTTGTGGAACTGGA 59.150 50.000 0.00 0.00 38.04 3.86
929 953 0.961019 CATGTGGGTTGTGGAACTGG 59.039 55.000 0.00 0.00 38.04 4.00
930 954 0.314935 GCATGTGGGTTGTGGAACTG 59.685 55.000 0.00 0.00 38.04 3.16
931 955 0.185901 AGCATGTGGGTTGTGGAACT 59.814 50.000 0.00 0.00 38.04 3.01
932 956 0.314935 CAGCATGTGGGTTGTGGAAC 59.685 55.000 0.00 0.00 37.35 3.62
1058 1082 5.378332 CAGCCTAAGCCTAGAGTTCTACTA 58.622 45.833 0.00 0.00 41.25 1.82
1059 1083 4.211920 CAGCCTAAGCCTAGAGTTCTACT 58.788 47.826 0.00 0.00 41.25 2.57
1060 1084 3.243602 GCAGCCTAAGCCTAGAGTTCTAC 60.244 52.174 0.00 0.00 41.25 2.59
1078 1102 0.679002 TGAATCCAAGGAGCAGCAGC 60.679 55.000 0.00 0.00 42.56 5.25
1079 1103 1.093159 GTGAATCCAAGGAGCAGCAG 58.907 55.000 0.00 0.00 0.00 4.24
1080 1104 0.401356 TGTGAATCCAAGGAGCAGCA 59.599 50.000 0.00 0.00 0.00 4.41
1179 1203 2.039405 GGTGCTGCTGCTCTTGGAG 61.039 63.158 17.00 0.00 40.48 3.86
1252 1285 0.116342 TCACCCTCACAAGCCTCCTA 59.884 55.000 0.00 0.00 0.00 2.94
1522 1555 2.038952 TGATCAAAGAGGTCTGTGGTGG 59.961 50.000 0.00 0.00 32.06 4.61
1579 1612 8.560374 GGGAGAGATGTACATTAATTAAGTTGC 58.440 37.037 10.30 0.00 0.00 4.17
1580 1613 9.838339 AGGGAGAGATGTACATTAATTAAGTTG 57.162 33.333 10.30 0.96 0.00 3.16
1590 1624 5.396884 GCAGGTAAAGGGAGAGATGTACATT 60.397 44.000 10.30 0.00 0.00 2.71
1806 1852 3.009805 GGATTTTACTAGGTGGTGGTGGT 59.990 47.826 0.00 0.00 0.00 4.16
2091 2142 9.709495 GTCTTGATCTGAGCAAAAGATAGATAT 57.291 33.333 9.82 0.00 34.50 1.63
2094 2145 6.038985 CGTCTTGATCTGAGCAAAAGATAGA 58.961 40.000 9.82 0.00 34.50 1.98
2095 2146 5.233902 CCGTCTTGATCTGAGCAAAAGATAG 59.766 44.000 9.82 3.67 34.50 2.08
2096 2147 5.105351 TCCGTCTTGATCTGAGCAAAAGATA 60.105 40.000 9.82 0.00 34.50 1.98
2097 2148 3.937706 CCGTCTTGATCTGAGCAAAAGAT 59.062 43.478 9.82 0.00 37.09 2.40
2148 2199 5.107065 GGTCTGAACTTTGTTAATGAGACCG 60.107 44.000 0.00 0.00 39.05 4.79
2289 2342 2.031012 CTGCCGTCCTTGCACTGA 59.969 61.111 0.00 0.00 34.46 3.41
2306 2359 0.326264 ACCTCACCAACCATCTCAGC 59.674 55.000 0.00 0.00 0.00 4.26
2310 2363 1.149101 AACCACCTCACCAACCATCT 58.851 50.000 0.00 0.00 0.00 2.90
2419 2473 0.605319 ATTCAAACGCTGCTTCCCGA 60.605 50.000 0.00 0.00 0.00 5.14
2560 2614 2.805671 CACGTGTCAGCTCAATTGGTTA 59.194 45.455 7.58 0.00 0.00 2.85
2617 2671 2.238521 TCTCCAACCTGGCAAACAATC 58.761 47.619 0.00 0.00 37.47 2.67
2654 2708 0.322008 CCAAGCTCCTCAGGTTCACC 60.322 60.000 0.00 0.00 38.33 4.02
2671 2725 2.285083 GTTTATAGCACGGCATCACCA 58.715 47.619 0.00 0.00 39.03 4.17
2757 2811 3.398406 TCAACTGAACACACGCACATAT 58.602 40.909 0.00 0.00 0.00 1.78
2764 2818 6.715464 ACTATTTTTCTCAACTGAACACACG 58.285 36.000 0.00 0.00 0.00 4.49
2828 2965 4.457834 AACAAACGAACAATTCCCAACA 57.542 36.364 0.00 0.00 0.00 3.33
2845 2982 6.072728 CGACCCTCATCTACAAATTCAAACAA 60.073 38.462 0.00 0.00 0.00 2.83
2858 2995 2.073252 ACTGATGCGACCCTCATCTA 57.927 50.000 4.85 0.00 40.59 1.98
2959 3096 1.010125 GAAACGCACGCTTTGAGCA 60.010 52.632 0.50 0.00 42.58 4.26
3068 3205 2.159572 CCTCCCGCAAACTACAAATTCG 60.160 50.000 0.00 0.00 0.00 3.34
3184 3322 6.989437 TCGTTAATCGTTTCATCTCATTCAC 58.011 36.000 0.00 0.00 40.80 3.18
3204 3342 8.850007 TGTACTCTGAGAAGCTATATATCGTT 57.150 34.615 12.44 0.00 0.00 3.85
3234 3374 3.340034 TCCATACAAAACCCACGACATC 58.660 45.455 0.00 0.00 0.00 3.06
3261 3401 9.859427 TGATCAATTCAAAATAAAACTAGCCTG 57.141 29.630 0.00 0.00 0.00 4.85
3423 3568 4.218417 GTGTACACGGGGAGTACTTAAGAA 59.782 45.833 10.84 0.00 41.76 2.52
3452 3597 4.911514 AAACTGCAAAAACGTCCTACAT 57.088 36.364 0.00 0.00 0.00 2.29
3457 3602 7.896894 TGTAAATTTAAACTGCAAAAACGTCC 58.103 30.769 0.00 0.00 0.00 4.79
3466 3611 9.204570 GTACTCTCTCTGTAAATTTAAACTGCA 57.795 33.333 0.00 0.00 0.00 4.41
3528 3701 4.792068 TCATACATCCTTCATTTGGTCCC 58.208 43.478 0.00 0.00 0.00 4.46
3532 3705 9.740239 CATAAACTTCATACATCCTTCATTTGG 57.260 33.333 0.00 0.00 0.00 3.28
3559 3732 7.349711 GTCGACTTTGTGCAAATCTAGTTTAA 58.650 34.615 8.70 0.00 0.00 1.52
3560 3733 6.346279 CGTCGACTTTGTGCAAATCTAGTTTA 60.346 38.462 14.70 0.00 0.00 2.01
3563 3736 3.428870 CGTCGACTTTGTGCAAATCTAGT 59.571 43.478 14.70 0.00 0.00 2.57
3571 3744 2.010670 CAACCGTCGACTTTGTGCA 58.989 52.632 14.70 0.00 0.00 4.57
3633 3806 3.616379 GCTTGCTTGTTTGTTTGTTAGCA 59.384 39.130 0.00 0.00 36.90 3.49
3653 3835 3.632145 AGTCCAAACGAAACTGAATTGCT 59.368 39.130 0.00 0.00 0.00 3.91
3804 4015 0.107456 AGAGCTGTGTGTTGGTGGAG 59.893 55.000 0.00 0.00 0.00 3.86
4344 4555 1.452833 GTGAATGGAGGAGCTGGGC 60.453 63.158 0.00 0.00 0.00 5.36
4345 4556 1.153289 CGTGAATGGAGGAGCTGGG 60.153 63.158 0.00 0.00 0.00 4.45
4346 4557 0.742281 CACGTGAATGGAGGAGCTGG 60.742 60.000 10.90 0.00 0.00 4.85
4347 4558 0.036952 ACACGTGAATGGAGGAGCTG 60.037 55.000 25.01 0.00 0.00 4.24
4348 4559 1.204941 GTACACGTGAATGGAGGAGCT 59.795 52.381 25.01 0.00 0.00 4.09
4349 4560 1.067142 TGTACACGTGAATGGAGGAGC 60.067 52.381 25.01 0.25 0.00 4.70
4350 4561 3.190079 CATGTACACGTGAATGGAGGAG 58.810 50.000 25.01 0.00 34.90 3.69
4351 4562 2.093711 CCATGTACACGTGAATGGAGGA 60.094 50.000 29.40 7.28 41.84 3.71
4352 4563 2.279741 CCATGTACACGTGAATGGAGG 58.720 52.381 29.40 18.19 41.84 4.30
4470 4681 2.310233 CGCCACAAGACAGACACCG 61.310 63.158 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.