Multiple sequence alignment - TraesCS4D01G145700

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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 TraesCS4D01G145700 chr4D 100.000 4549 0 0 1 4549 134639014 134634466 0.000000e+00 8401.0
1 TraesCS4D01G145700 chr4D 85.227 176 25 1 63 238 97873497 97873671 3.620000e-41 180.0
2 TraesCS4D01G145700 chr4D 98.113 53 0 1 4305 4357 134634662 134634611 1.740000e-14 91.6
3 TraesCS4D01G145700 chr4D 98.113 53 0 1 4353 4404 134634710 134634658 1.740000e-14 91.6
4 TraesCS4D01G145700 chr4A 94.104 3443 146 22 236 3672 396755581 396752190 0.000000e+00 5180.0
5 TraesCS4D01G145700 chr4A 93.571 140 6 1 3685 3824 396752116 396751980 5.970000e-49 206.0
6 TraesCS4D01G145700 chr4B 92.946 1531 42 18 2142 3672 193546146 193544682 0.000000e+00 2169.0
7 TraesCS4D01G145700 chr4B 95.757 1249 29 9 875 2112 193547473 193546238 0.000000e+00 1991.0
8 TraesCS4D01G145700 chr4B 88.262 673 56 10 6 670 193548756 193548099 0.000000e+00 784.0
9 TraesCS4D01G145700 chr4B 94.475 181 10 0 4369 4549 193543592 193543412 3.470000e-71 279.0
10 TraesCS4D01G145700 chr4B 88.987 227 22 2 3857 4080 193544060 193543834 1.250000e-70 278.0
11 TraesCS4D01G145700 chr4B 91.919 198 12 2 4066 4260 193543815 193543619 1.610000e-69 274.0
12 TraesCS4D01G145700 chr4B 90.452 199 16 2 683 880 193548148 193547952 4.510000e-65 259.0
13 TraesCS4D01G145700 chr4B 91.837 147 9 2 3709 3855 193544489 193544346 7.720000e-48 202.0
14 TraesCS4D01G145700 chr5A 89.326 178 19 0 59 236 458995622 458995799 1.650000e-54 224.0
15 TraesCS4D01G145700 chr6D 87.778 180 22 0 59 238 266748919 266748740 1.280000e-50 211.0
16 TraesCS4D01G145700 chr5D 86.517 178 24 0 59 236 58518149 58518326 3.590000e-46 196.0
17 TraesCS4D01G145700 chr7D 85.083 181 25 2 59 238 512128989 512128810 2.800000e-42 183.0
18 TraesCS4D01G145700 chr5B 85.965 171 24 0 60 230 621978725 621978895 2.800000e-42 183.0
19 TraesCS4D01G145700 chr2D 85.000 180 27 0 59 238 286667852 286667673 2.800000e-42 183.0
20 TraesCS4D01G145700 chr3B 84.530 181 28 0 59 239 611141093 611140913 3.620000e-41 180.0
21 TraesCS4D01G145700 chr6B 80.000 140 26 2 3914 4053 171714750 171714887 8.050000e-18 102.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G145700 chr4D 134634466 134639014 4548 True 8401.0 8401 100.000000 1 4549 1 chr4D.!!$R1 4548
1 TraesCS4D01G145700 chr4A 396751980 396755581 3601 True 2693.0 5180 93.837500 236 3824 2 chr4A.!!$R1 3588
2 TraesCS4D01G145700 chr4B 193543412 193548756 5344 True 779.5 2169 91.829375 6 4549 8 chr4B.!!$R1 4543

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
677 686 0.109153 TGATGGAGCATCATTCGGGG 59.891 55.000 0.0 0.0 44.6 5.73 F
1019 1572 0.445436 GTCAGCAGCCAGATCAAACG 59.555 55.000 0.0 0.0 0.0 3.60 F
1893 2455 0.868406 GGAGAGGTTTGCAGTTGTCG 59.132 55.000 0.0 0.0 0.0 4.35 F
2326 2950 1.135199 TCCGTTCTGTTACATCTCGCC 60.135 52.381 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2575 0.950555 CACGCTTGCAGCCTCTAACA 60.951 55.000 0.00 0.0 38.18 2.41 R
2208 2832 1.359130 AGCTTAGTGAGGCCCCAAAAT 59.641 47.619 0.00 0.0 0.00 1.82 R
3139 3763 0.320683 CACATCCGGTCAAGAGCACA 60.321 55.000 0.00 0.0 0.00 4.57 R
4111 5215 0.106167 AGGGGACGATGCTAGCACTA 60.106 55.000 22.07 0.0 0.00 2.74 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
52 57 4.828925 GAGGCCACCGCAGAGCTC 62.829 72.222 5.01 5.27 36.38 4.09
79 84 2.668550 GGCGCCCCCATATTCGTC 60.669 66.667 18.11 0.00 0.00 4.20
136 141 3.665190 CCCGAGTATTTGAGGGCTATTC 58.335 50.000 0.00 0.00 37.07 1.75
163 168 0.949105 CCGTCTGGGTCCAACTTTCG 60.949 60.000 0.00 0.00 0.00 3.46
166 171 1.124780 TCTGGGTCCAACTTTCGTGA 58.875 50.000 0.00 0.00 0.00 4.35
167 172 1.202604 TCTGGGTCCAACTTTCGTGAC 60.203 52.381 0.00 0.00 0.00 3.67
168 173 0.834612 TGGGTCCAACTTTCGTGACT 59.165 50.000 0.00 0.00 0.00 3.41
169 174 1.226746 GGGTCCAACTTTCGTGACTG 58.773 55.000 0.00 0.00 0.00 3.51
170 175 1.226746 GGTCCAACTTTCGTGACTGG 58.773 55.000 0.00 0.00 0.00 4.00
171 176 1.226746 GTCCAACTTTCGTGACTGGG 58.773 55.000 0.00 0.00 0.00 4.45
172 177 0.534203 TCCAACTTTCGTGACTGGGC 60.534 55.000 0.00 0.00 0.00 5.36
173 178 0.817634 CCAACTTTCGTGACTGGGCA 60.818 55.000 0.00 0.00 0.00 5.36
174 179 0.588252 CAACTTTCGTGACTGGGCAG 59.412 55.000 0.00 0.00 0.00 4.85
175 180 1.166531 AACTTTCGTGACTGGGCAGC 61.167 55.000 0.00 0.00 0.00 5.25
176 181 1.302033 CTTTCGTGACTGGGCAGCT 60.302 57.895 0.00 0.00 0.00 4.24
220 225 1.152096 AGACGGGTTTGAGGGGTCT 60.152 57.895 0.00 0.00 33.38 3.85
298 303 1.378762 CCACCGTCCATCCACCTTT 59.621 57.895 0.00 0.00 0.00 3.11
318 323 0.544357 TCCCTTTTCTCTCTCGGCCA 60.544 55.000 2.24 0.00 0.00 5.36
352 361 2.202932 CCAATCCGCAGAGTCCCG 60.203 66.667 0.00 0.00 0.00 5.14
402 411 1.457346 CAATCAGCAACCCACCTCTC 58.543 55.000 0.00 0.00 0.00 3.20
435 444 2.036414 TCTGCCCTCTCGCACTCT 59.964 61.111 0.00 0.00 34.35 3.24
452 461 0.321671 TCTCAGCGGCTAAGTTGCTT 59.678 50.000 0.26 0.00 36.69 3.91
486 495 2.033141 AGAGCCGTGCATTGCTGT 59.967 55.556 16.53 10.49 38.11 4.40
513 522 4.175489 GCTGCTGCGCTGTGATGG 62.175 66.667 16.05 3.50 0.00 3.51
570 579 3.434739 GGATGTTCCAATCAGAGGCTCAT 60.435 47.826 18.26 0.00 36.28 2.90
574 583 2.475155 TCCAATCAGAGGCTCATCAGT 58.525 47.619 18.26 0.00 0.00 3.41
575 584 2.842496 TCCAATCAGAGGCTCATCAGTT 59.158 45.455 18.26 1.23 0.00 3.16
658 667 3.390521 TCGGGCCTCGATTGCTGT 61.391 61.111 11.66 0.00 43.74 4.40
659 668 3.197790 CGGGCCTCGATTGCTGTG 61.198 66.667 0.84 0.00 42.43 3.66
660 669 2.268920 GGGCCTCGATTGCTGTGA 59.731 61.111 0.84 0.00 0.00 3.58
661 670 1.153086 GGGCCTCGATTGCTGTGAT 60.153 57.895 0.84 0.00 0.00 3.06
662 671 1.442526 GGGCCTCGATTGCTGTGATG 61.443 60.000 0.84 0.00 0.00 3.07
663 672 1.442526 GGCCTCGATTGCTGTGATGG 61.443 60.000 0.00 0.00 0.00 3.51
664 673 0.462581 GCCTCGATTGCTGTGATGGA 60.463 55.000 0.15 0.00 0.00 3.41
665 674 1.579698 CCTCGATTGCTGTGATGGAG 58.420 55.000 0.00 0.00 0.00 3.86
666 675 0.935898 CTCGATTGCTGTGATGGAGC 59.064 55.000 0.00 0.00 36.95 4.70
667 676 0.249955 TCGATTGCTGTGATGGAGCA 59.750 50.000 0.00 0.00 44.75 4.26
668 677 1.134310 TCGATTGCTGTGATGGAGCAT 60.134 47.619 0.00 0.00 45.69 3.79
669 678 1.263484 CGATTGCTGTGATGGAGCATC 59.737 52.381 0.00 0.00 45.69 3.91
670 679 2.294979 GATTGCTGTGATGGAGCATCA 58.705 47.619 0.00 0.00 46.84 3.07
676 685 3.711937 TGATGGAGCATCATTCGGG 57.288 52.632 0.00 0.00 44.60 5.14
677 686 0.109153 TGATGGAGCATCATTCGGGG 59.891 55.000 0.00 0.00 44.60 5.73
678 687 1.228367 ATGGAGCATCATTCGGGGC 60.228 57.895 0.00 0.00 36.25 5.80
679 688 2.595754 GGAGCATCATTCGGGGCC 60.596 66.667 0.00 0.00 36.25 5.80
680 689 2.974698 GAGCATCATTCGGGGCCG 60.975 66.667 0.00 0.00 36.33 6.13
744 813 2.029470 GGAGCATCTCTGGATAGGAACG 60.029 54.545 0.00 0.00 33.73 3.95
811 880 1.073964 CTGCTGTGACAGATCAACGG 58.926 55.000 18.18 0.00 40.25 4.44
861 930 4.082136 GGTAGGGTATCAGTCGGATGATTC 60.082 50.000 8.29 4.31 40.40 2.52
873 942 0.875908 GATGATTCGTAGCAGCGCCA 60.876 55.000 2.29 0.00 0.00 5.69
915 1466 7.315890 GCTACTCAGCCACATTTATTTTTCTT 58.684 34.615 0.00 0.00 42.37 2.52
1019 1572 0.445436 GTCAGCAGCCAGATCAAACG 59.555 55.000 0.00 0.00 0.00 3.60
1463 2016 2.637947 TGCTCACAAGTTGTTACTGCA 58.362 42.857 5.57 11.16 34.01 4.41
1641 2195 3.588569 AGTCTACTTGAGGGGTGAAACT 58.411 45.455 0.00 0.00 36.74 2.66
1860 2422 2.209273 TGATGATTTGCGTGTATCCGG 58.791 47.619 0.00 0.00 0.00 5.14
1893 2455 0.868406 GGAGAGGTTTGCAGTTGTCG 59.132 55.000 0.00 0.00 0.00 4.35
2013 2575 9.846248 GTTGCATTGATTTAGTGAGATAAGTTT 57.154 29.630 0.00 0.00 0.00 2.66
2065 2627 7.847096 TGTGATTCAACCTATTAGCTTCTGTA 58.153 34.615 0.00 0.00 0.00 2.74
2094 2656 9.726232 CTACGCTATGAAGTTTATGTTGTACTA 57.274 33.333 0.00 0.00 0.00 1.82
2095 2657 8.403606 ACGCTATGAAGTTTATGTTGTACTAC 57.596 34.615 0.05 0.05 0.00 2.73
2096 2658 8.248945 ACGCTATGAAGTTTATGTTGTACTACT 58.751 33.333 8.88 0.00 0.00 2.57
2208 2832 6.946340 TGGAGTTCATCTTTCTGCAGTATTA 58.054 36.000 14.67 0.00 0.00 0.98
2264 2888 9.959721 ATACTTACATAGTCCACATTTGAAAGT 57.040 29.630 0.00 0.00 38.33 2.66
2324 2948 3.211803 TGTCCGTTCTGTTACATCTCG 57.788 47.619 0.00 0.00 0.00 4.04
2325 2949 1.918609 GTCCGTTCTGTTACATCTCGC 59.081 52.381 0.00 0.00 0.00 5.03
2326 2950 1.135199 TCCGTTCTGTTACATCTCGCC 60.135 52.381 0.00 0.00 0.00 5.54
2329 2953 2.345641 CGTTCTGTTACATCTCGCCTTG 59.654 50.000 0.00 0.00 0.00 3.61
2330 2954 3.326747 GTTCTGTTACATCTCGCCTTGT 58.673 45.455 0.00 0.00 0.00 3.16
2331 2955 3.678056 TCTGTTACATCTCGCCTTGTT 57.322 42.857 0.00 0.00 0.00 2.83
2332 2956 4.794278 TCTGTTACATCTCGCCTTGTTA 57.206 40.909 0.00 0.00 0.00 2.41
2333 2957 5.142061 TCTGTTACATCTCGCCTTGTTAA 57.858 39.130 0.00 0.00 0.00 2.01
2358 2982 9.773328 AATATGAATCACATTGTTACTTTCACG 57.227 29.630 0.00 0.00 40.07 4.35
2367 2991 6.643770 ACATTGTTACTTTCACGATCGTACTT 59.356 34.615 22.26 6.36 0.00 2.24
2433 3057 3.747854 TGCTGGAAATTGCAACAATGA 57.252 38.095 0.00 0.00 36.15 2.57
2435 3059 3.181468 TGCTGGAAATTGCAACAATGACA 60.181 39.130 0.00 0.00 36.15 3.58
2501 3125 9.316730 ACGAATGTGTACTTTACTTTTTACAGA 57.683 29.630 0.00 0.00 0.00 3.41
2540 3164 7.274447 TGTTCTGACACATGCATGATCTATAA 58.726 34.615 32.75 18.59 0.00 0.98
2545 3169 8.181904 TGACACATGCATGATCTATAACTAGA 57.818 34.615 32.75 7.84 38.34 2.43
2554 3178 9.096160 GCATGATCTATAACTAGATTGACATGG 57.904 37.037 16.45 6.49 43.35 3.66
2590 3214 4.141597 TGCAGTCGATATATTTTGGTGGGA 60.142 41.667 0.00 0.00 0.00 4.37
2593 3217 6.653320 GCAGTCGATATATTTTGGTGGGATAA 59.347 38.462 0.00 0.00 0.00 1.75
2599 3223 9.456147 CGATATATTTTGGTGGGATAATGGTTA 57.544 33.333 0.00 0.00 0.00 2.85
2613 3237 7.420800 GGATAATGGTTATTGCTTGAGTCTTG 58.579 38.462 0.00 0.00 0.00 3.02
2677 3301 9.706691 CCGAAACCTTGACTATGTATGTATATT 57.293 33.333 0.00 0.00 0.00 1.28
2717 3341 6.868864 CCAATTAGCTAGCACATACTACGAAT 59.131 38.462 18.83 0.00 0.00 3.34
2731 3355 5.862924 ACTACGAATGAAACCTGTGAATG 57.137 39.130 0.00 0.00 0.00 2.67
2741 3365 3.737559 ACCTGTGAATGAATTGCCCTA 57.262 42.857 0.00 0.00 0.00 3.53
2752 3376 7.178983 TGAATGAATTGCCCTAGTTTTTCTGAT 59.821 33.333 0.00 0.00 0.00 2.90
2789 3413 8.902540 TCAGTCTGTCAATTTGTATACACTTT 57.097 30.769 4.68 0.00 0.00 2.66
2790 3414 8.773645 TCAGTCTGTCAATTTGTATACACTTTG 58.226 33.333 4.68 12.02 0.00 2.77
2791 3415 8.559536 CAGTCTGTCAATTTGTATACACTTTGT 58.440 33.333 19.15 4.39 0.00 2.83
2792 3416 8.774586 AGTCTGTCAATTTGTATACACTTTGTC 58.225 33.333 19.15 16.00 0.00 3.18
2795 3419 9.729023 CTGTCAATTTGTATACACTTTGTCAAA 57.271 29.630 19.15 0.00 30.01 2.69
2796 3420 9.509855 TGTCAATTTGTATACACTTTGTCAAAC 57.490 29.630 19.15 13.49 28.76 2.93
2797 3421 9.509855 GTCAATTTGTATACACTTTGTCAAACA 57.490 29.630 19.15 4.39 28.76 2.83
2798 3422 9.729023 TCAATTTGTATACACTTTGTCAAACAG 57.271 29.630 19.15 0.00 28.76 3.16
2799 3423 8.967218 CAATTTGTATACACTTTGTCAAACAGG 58.033 33.333 4.68 0.00 28.76 4.00
2800 3424 7.633193 TTTGTATACACTTTGTCAAACAGGT 57.367 32.000 4.68 0.00 0.00 4.00
2801 3425 7.633193 TTGTATACACTTTGTCAAACAGGTT 57.367 32.000 4.68 0.00 0.00 3.50
2802 3426 7.022055 TGTATACACTTTGTCAAACAGGTTG 57.978 36.000 0.08 0.00 38.71 3.77
2803 3427 6.824196 TGTATACACTTTGTCAAACAGGTTGA 59.176 34.615 0.08 0.00 44.20 3.18
2815 3439 7.504924 TCAAACAGGTTGAGTTATTAACAGG 57.495 36.000 9.15 0.00 41.47 4.00
3178 3802 1.754803 GACGACTCCCACATCCACATA 59.245 52.381 0.00 0.00 0.00 2.29
3532 4156 2.494471 TGTTCTACCATGACCTGTACCG 59.506 50.000 0.00 0.00 0.00 4.02
3556 4180 0.246635 ACGATGCTGACTAAAGCCGT 59.753 50.000 0.00 0.00 42.83 5.68
3637 4262 4.717233 TGCGACATGCTTATTTGGATTT 57.283 36.364 0.00 0.00 46.63 2.17
3717 4473 2.736144 TAGCTCAGTTAACACCCACG 57.264 50.000 8.61 0.00 0.00 4.94
3723 4479 0.107116 AGTTAACACCCACGCCAACA 60.107 50.000 8.61 0.00 0.00 3.33
3725 4481 0.955178 TTAACACCCACGCCAACATG 59.045 50.000 0.00 0.00 0.00 3.21
3726 4482 0.179015 TAACACCCACGCCAACATGT 60.179 50.000 0.00 0.00 0.00 3.21
3727 4483 1.040339 AACACCCACGCCAACATGTT 61.040 50.000 4.92 4.92 0.00 2.71
3728 4484 0.179015 ACACCCACGCCAACATGTTA 60.179 50.000 11.53 0.00 0.00 2.41
3729 4485 0.521291 CACCCACGCCAACATGTTAG 59.479 55.000 11.53 5.02 0.00 2.34
3735 4519 4.247258 CCACGCCAACATGTTAGTACTTA 58.753 43.478 11.53 0.00 0.00 2.24
3772 4556 3.063452 ACTGCTTCGTTGGCATAAATACG 59.937 43.478 2.39 2.39 39.07 3.06
3856 4640 9.745018 ATAGTTTTCATCTCAAATCCTTCTTGA 57.255 29.630 0.00 0.00 0.00 3.02
3857 4641 8.647256 AGTTTTCATCTCAAATCCTTCTTGAT 57.353 30.769 0.00 0.00 32.53 2.57
3858 4642 8.521176 AGTTTTCATCTCAAATCCTTCTTGATG 58.479 33.333 0.00 0.00 32.53 3.07
3859 4643 8.302438 GTTTTCATCTCAAATCCTTCTTGATGT 58.698 33.333 0.00 0.00 32.53 3.06
3862 4646 7.046652 TCATCTCAAATCCTTCTTGATGTCTC 58.953 38.462 0.00 0.00 32.53 3.36
3863 4647 6.364568 TCTCAAATCCTTCTTGATGTCTCA 57.635 37.500 0.00 0.00 32.53 3.27
3866 4936 8.542926 TCTCAAATCCTTCTTGATGTCTCAATA 58.457 33.333 0.00 0.00 40.52 1.90
3881 4951 7.395190 TGTCTCAATACCCTGATTTTCAATG 57.605 36.000 0.00 0.00 0.00 2.82
3892 4962 8.370182 ACCCTGATTTTCAATGCCATATAATTC 58.630 33.333 0.00 0.00 0.00 2.17
3912 4982 1.443194 GCGGACGCTACTTGTCGAA 60.443 57.895 9.76 0.00 37.22 3.71
3919 4989 2.230508 ACGCTACTTGTCGAAAGGATGA 59.769 45.455 10.65 0.00 0.00 2.92
3929 4999 3.127030 GTCGAAAGGATGATGTTTGGGTC 59.873 47.826 0.00 0.00 0.00 4.46
3966 5036 2.562912 CTGTTGGATGGCACGTGC 59.437 61.111 32.15 32.15 41.14 5.34
3971 5041 3.047280 GGATGGCACGTGCGACAA 61.047 61.111 32.35 18.81 43.26 3.18
3977 5047 2.657296 CACGTGCGACAACCGTCT 60.657 61.111 0.82 0.00 40.23 4.18
3979 5049 2.657296 CGTGCGACAACCGTCTGT 60.657 61.111 0.00 0.00 40.23 3.41
3984 5054 0.318784 GCGACAACCGTCTGTTCTCT 60.319 55.000 0.00 0.00 40.23 3.10
3988 5058 1.006102 AACCGTCTGTTCTCTGCCG 60.006 57.895 0.00 0.00 28.45 5.69
3997 5067 3.876589 TTCTCTGCCGGCGTTGACC 62.877 63.158 23.90 0.00 0.00 4.02
4030 5100 0.450184 ACAAAGAACGTGTTGCGCTT 59.550 45.000 9.73 0.00 46.11 4.68
4032 5102 0.730265 AAAGAACGTGTTGCGCTTGA 59.270 45.000 9.73 0.00 46.11 3.02
4049 5119 1.081840 GAGGCTTTGCAACACGAGC 60.082 57.895 11.60 11.60 0.00 5.03
4063 5133 3.730761 GAGCTGTGTTGCTGCCCG 61.731 66.667 0.00 0.00 44.17 6.13
4064 5134 4.569180 AGCTGTGTTGCTGCCCGT 62.569 61.111 0.00 0.00 42.33 5.28
4083 5187 2.034124 GTCCATTGCAACATAGCCCAT 58.966 47.619 0.00 0.00 0.00 4.00
4110 5214 4.509616 CGGACAATATGGACAAGGTGTTA 58.490 43.478 0.00 0.00 0.00 2.41
4111 5215 5.123227 CGGACAATATGGACAAGGTGTTAT 58.877 41.667 0.00 0.00 0.00 1.89
4130 5234 0.106167 TAGTGCTAGCATCGTCCCCT 60.106 55.000 22.51 13.52 0.00 4.79
4159 5266 1.685355 AAAACCTTGCAGCACCACCC 61.685 55.000 0.00 0.00 0.00 4.61
4194 5301 1.284297 GCGCCAATGACAACCTTTGC 61.284 55.000 0.00 0.00 0.00 3.68
4200 5307 0.593128 ATGACAACCTTTGCTGCGAC 59.407 50.000 0.00 0.00 0.00 5.19
4233 5340 1.067565 TGTAGCAAAGCTCTCGGACAG 60.068 52.381 0.00 0.00 40.44 3.51
4277 5384 3.474570 CGAAGGAGAGCCCCTGGG 61.475 72.222 5.50 5.50 36.49 4.45
4278 5385 2.285743 GAAGGAGAGCCCCTGGGT 60.286 66.667 12.71 0.00 36.49 4.51
4279 5386 2.612115 AAGGAGAGCCCCTGGGTG 60.612 66.667 12.71 4.35 36.49 4.61
4280 5387 3.194025 AAGGAGAGCCCCTGGGTGA 62.194 63.158 12.71 0.00 36.49 4.02
4281 5388 2.610859 GGAGAGCCCCTGGGTGAA 60.611 66.667 12.71 0.00 37.65 3.18
4282 5389 2.231380 GGAGAGCCCCTGGGTGAAA 61.231 63.158 12.71 0.00 37.65 2.69
4294 5401 2.751688 GTGAAACCCCCTGCCGTA 59.248 61.111 0.00 0.00 0.00 4.02
4295 5402 1.376812 GTGAAACCCCCTGCCGTAG 60.377 63.158 0.00 0.00 0.00 3.51
4308 5415 2.439701 CGTAGGGGAGCGTGAGGA 60.440 66.667 0.00 0.00 0.00 3.71
4309 5416 2.772691 CGTAGGGGAGCGTGAGGAC 61.773 68.421 0.00 0.00 0.00 3.85
4310 5417 1.681327 GTAGGGGAGCGTGAGGACA 60.681 63.158 0.00 0.00 0.00 4.02
4311 5418 1.043673 GTAGGGGAGCGTGAGGACAT 61.044 60.000 0.00 0.00 0.00 3.06
4312 5419 1.043116 TAGGGGAGCGTGAGGACATG 61.043 60.000 0.00 0.00 36.24 3.21
4313 5420 2.359169 GGGGAGCGTGAGGACATGA 61.359 63.158 0.00 0.00 35.25 3.07
4314 5421 1.142748 GGGAGCGTGAGGACATGAG 59.857 63.158 0.00 0.00 35.25 2.90
4315 5422 1.520342 GGAGCGTGAGGACATGAGC 60.520 63.158 0.00 0.00 35.25 4.26
4316 5423 1.216444 GAGCGTGAGGACATGAGCA 59.784 57.895 0.00 0.00 35.25 4.26
4317 5424 0.805322 GAGCGTGAGGACATGAGCAG 60.805 60.000 0.00 0.00 35.25 4.24
4318 5425 2.459442 GCGTGAGGACATGAGCAGC 61.459 63.158 0.00 0.00 35.25 5.25
4319 5426 1.812922 CGTGAGGACATGAGCAGCC 60.813 63.158 0.00 0.00 35.25 4.85
4320 5427 1.812922 GTGAGGACATGAGCAGCCG 60.813 63.158 0.00 0.00 0.00 5.52
4321 5428 2.894387 GAGGACATGAGCAGCCGC 60.894 66.667 0.00 0.00 38.99 6.53
4322 5429 4.479993 AGGACATGAGCAGCCGCC 62.480 66.667 0.00 0.00 39.83 6.13
4323 5430 4.479993 GGACATGAGCAGCCGCCT 62.480 66.667 0.00 0.00 39.83 5.52
4324 5431 3.200593 GACATGAGCAGCCGCCTG 61.201 66.667 0.00 0.00 42.13 4.85
4332 5439 2.359850 CAGCCGCCTGCCAAAGTA 60.360 61.111 0.00 0.00 42.71 2.24
4333 5440 2.045926 AGCCGCCTGCCAAAGTAG 60.046 61.111 0.00 0.00 42.71 2.57
4344 5451 5.619625 CTGCCAAAGTAGGAGAGAAAAAG 57.380 43.478 0.00 0.00 0.00 2.27
4345 5452 3.821033 TGCCAAAGTAGGAGAGAAAAAGC 59.179 43.478 0.00 0.00 0.00 3.51
4346 5453 3.120165 GCCAAAGTAGGAGAGAAAAAGCG 60.120 47.826 0.00 0.00 0.00 4.68
4347 5454 4.315803 CCAAAGTAGGAGAGAAAAAGCGA 58.684 43.478 0.00 0.00 0.00 4.93
4348 5455 4.755123 CCAAAGTAGGAGAGAAAAAGCGAA 59.245 41.667 0.00 0.00 0.00 4.70
4349 5456 5.106908 CCAAAGTAGGAGAGAAAAAGCGAAG 60.107 44.000 0.00 0.00 0.00 3.79
4350 5457 4.195225 AGTAGGAGAGAAAAAGCGAAGG 57.805 45.455 0.00 0.00 0.00 3.46
4351 5458 2.481289 AGGAGAGAAAAAGCGAAGGG 57.519 50.000 0.00 0.00 0.00 3.95
4352 5459 1.003696 AGGAGAGAAAAAGCGAAGGGG 59.996 52.381 0.00 0.00 0.00 4.79
4353 5460 1.003233 GGAGAGAAAAAGCGAAGGGGA 59.997 52.381 0.00 0.00 0.00 4.81
4354 5461 2.351455 GAGAGAAAAAGCGAAGGGGAG 58.649 52.381 0.00 0.00 0.00 4.30
4355 5462 1.003696 AGAGAAAAAGCGAAGGGGAGG 59.996 52.381 0.00 0.00 0.00 4.30
4356 5463 1.003233 GAGAAAAAGCGAAGGGGAGGA 59.997 52.381 0.00 0.00 0.00 3.71
4357 5464 1.166129 GAAAAAGCGAAGGGGAGGAC 58.834 55.000 0.00 0.00 0.00 3.85
4358 5465 0.476771 AAAAAGCGAAGGGGAGGACA 59.523 50.000 0.00 0.00 0.00 4.02
4359 5466 0.698818 AAAAGCGAAGGGGAGGACAT 59.301 50.000 0.00 0.00 0.00 3.06
4360 5467 0.035056 AAAGCGAAGGGGAGGACATG 60.035 55.000 0.00 0.00 0.00 3.21
4361 5468 0.909610 AAGCGAAGGGGAGGACATGA 60.910 55.000 0.00 0.00 0.00 3.07
4362 5469 1.144936 GCGAAGGGGAGGACATGAG 59.855 63.158 0.00 0.00 0.00 2.90
4363 5470 1.144936 CGAAGGGGAGGACATGAGC 59.855 63.158 0.00 0.00 0.00 4.26
4364 5471 1.617018 CGAAGGGGAGGACATGAGCA 61.617 60.000 0.00 0.00 0.00 4.26
4365 5472 0.179936 GAAGGGGAGGACATGAGCAG 59.820 60.000 0.00 0.00 0.00 4.24
4366 5473 1.919600 AAGGGGAGGACATGAGCAGC 61.920 60.000 0.00 0.00 0.00 5.25
4367 5474 2.191641 GGGAGGACATGAGCAGCC 59.808 66.667 0.00 0.00 0.00 4.85
4381 5488 2.045926 AGCCGCCTGCCAAAGTAG 60.046 61.111 0.00 0.00 42.71 2.57
4439 5546 5.783111 CAAGGGGATAAAGTTTCACAAAGG 58.217 41.667 0.00 0.00 0.00 3.11
4443 5550 6.385759 AGGGGATAAAGTTTCACAAAGGTTTT 59.614 34.615 0.00 0.00 0.00 2.43
4497 5604 3.699779 TCAATCTGAAGAGATCCGACG 57.300 47.619 0.00 0.00 38.03 5.12
4524 5631 2.307309 CGTGACCGACGCAACATGT 61.307 57.895 0.00 0.00 42.21 3.21
4526 5633 1.068250 TGACCGACGCAACATGTCA 59.932 52.632 0.00 0.00 36.11 3.58
4533 5640 2.472886 CGACGCAACATGTCAATCAGTC 60.473 50.000 0.00 3.09 36.11 3.51
4534 5641 1.460743 ACGCAACATGTCAATCAGTCG 59.539 47.619 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.699522 AGGGGCTCGTCAAACGCC 62.700 66.667 0.00 0.00 42.21 5.68
43 44 2.420890 GGGGAGATGAGCTCTGCG 59.579 66.667 16.19 0.00 42.94 5.18
47 48 3.934962 GCCCGGGGAGATGAGCTC 61.935 72.222 25.28 6.82 43.17 4.09
78 83 5.183530 CCATATCCAGCTCAAATATGGGA 57.816 43.478 21.00 8.58 44.48 4.37
109 114 1.473434 CCTCAAATACTCGGGCTGACC 60.473 57.143 0.00 0.00 0.00 4.02
110 115 1.473434 CCCTCAAATACTCGGGCTGAC 60.473 57.143 0.00 0.00 0.00 3.51
111 116 0.830648 CCCTCAAATACTCGGGCTGA 59.169 55.000 0.00 0.00 0.00 4.26
112 117 3.386543 CCCTCAAATACTCGGGCTG 57.613 57.895 0.00 0.00 0.00 4.85
115 120 3.665190 GAATAGCCCTCAAATACTCGGG 58.335 50.000 0.00 0.00 39.76 5.14
116 121 3.005472 TCGAATAGCCCTCAAATACTCGG 59.995 47.826 0.00 0.00 0.00 4.63
117 122 4.230657 CTCGAATAGCCCTCAAATACTCG 58.769 47.826 0.00 0.00 0.00 4.18
119 124 3.325135 CCCTCGAATAGCCCTCAAATACT 59.675 47.826 0.00 0.00 0.00 2.12
121 126 2.637872 CCCCTCGAATAGCCCTCAAATA 59.362 50.000 0.00 0.00 0.00 1.40
122 127 1.421646 CCCCTCGAATAGCCCTCAAAT 59.578 52.381 0.00 0.00 0.00 2.32
131 136 1.833049 AGACGGGCCCCTCGAATAG 60.833 63.158 18.66 0.96 0.00 1.73
132 137 2.131709 CAGACGGGCCCCTCGAATA 61.132 63.158 18.66 0.00 0.00 1.75
133 138 3.470888 CAGACGGGCCCCTCGAAT 61.471 66.667 18.66 0.00 0.00 3.34
158 163 0.037326 TAGCTGCCCAGTCACGAAAG 60.037 55.000 0.00 0.00 0.00 2.62
163 168 2.125512 CGGTAGCTGCCCAGTCAC 60.126 66.667 15.92 0.00 0.00 3.67
189 194 3.110178 CGTCTCAAACGTCCGGGC 61.110 66.667 0.00 0.00 46.42 6.13
298 303 0.613777 GGCCGAGAGAGAAAAGGGAA 59.386 55.000 0.00 0.00 0.00 3.97
318 323 1.056660 TGGAAGGAAGAAGACGGCTT 58.943 50.000 1.10 1.10 36.96 4.35
352 361 1.822371 GAGAGAGGAGAAGGGTGTCAC 59.178 57.143 0.00 0.00 0.00 3.67
402 411 0.397816 CAGAGTGTAGGGGAGAGGGG 60.398 65.000 0.00 0.00 0.00 4.79
435 444 0.321671 AGAAGCAACTTAGCCGCTGA 59.678 50.000 2.16 0.00 35.79 4.26
443 452 2.032634 CCGCGGCAGAAGCAACTTA 61.033 57.895 14.67 0.00 44.61 2.24
466 475 3.437795 GCAATGCACGGCTCTGCT 61.438 61.111 0.00 0.00 38.07 4.24
475 484 1.310933 CCCTCCTCACAGCAATGCAC 61.311 60.000 8.35 0.00 0.00 4.57
529 538 0.859232 CACTCCAACTTTGTCGTCGG 59.141 55.000 0.00 0.00 0.00 4.79
575 584 4.877378 AGGATGATGCTGCAAAGAAAAA 57.123 36.364 6.36 0.00 0.00 1.94
580 589 1.922570 GCAAGGATGATGCTGCAAAG 58.077 50.000 6.36 0.00 40.64 2.77
659 668 1.239968 GCCCCGAATGATGCTCCATC 61.240 60.000 0.00 0.00 40.88 3.51
660 669 1.228367 GCCCCGAATGATGCTCCAT 60.228 57.895 0.00 0.00 0.00 3.41
661 670 2.192979 GCCCCGAATGATGCTCCA 59.807 61.111 0.00 0.00 0.00 3.86
662 671 2.595754 GGCCCCGAATGATGCTCC 60.596 66.667 0.00 0.00 0.00 4.70
663 672 2.974698 CGGCCCCGAATGATGCTC 60.975 66.667 0.00 0.00 42.83 4.26
706 715 4.980903 CAACGCAACGTGCAGCCC 62.981 66.667 9.95 0.00 45.36 5.19
707 716 4.980903 CCAACGCAACGTGCAGCC 62.981 66.667 9.95 0.00 45.36 4.85
708 717 3.862063 CTCCAACGCAACGTGCAGC 62.862 63.158 9.95 4.62 45.36 5.25
709 718 2.249309 CTCCAACGCAACGTGCAG 59.751 61.111 9.95 5.83 45.36 4.41
710 719 3.947841 GCTCCAACGCAACGTGCA 61.948 61.111 9.95 0.00 45.36 4.57
711 720 3.254014 ATGCTCCAACGCAACGTGC 62.254 57.895 0.00 0.00 44.06 5.34
712 721 1.154413 GATGCTCCAACGCAACGTG 60.154 57.895 0.00 0.00 44.06 4.49
713 722 1.291877 GAGATGCTCCAACGCAACGT 61.292 55.000 0.00 0.00 44.06 3.99
714 723 1.016130 AGAGATGCTCCAACGCAACG 61.016 55.000 0.00 0.00 44.06 4.10
744 813 1.639298 GCTCATGTTGTCGGACAGGC 61.639 60.000 11.14 9.04 31.79 4.85
747 816 1.374125 CCGCTCATGTTGTCGGACA 60.374 57.895 6.76 6.76 44.23 4.02
811 880 1.805945 GGACCGACGACACTGCATC 60.806 63.158 0.00 0.00 0.00 3.91
840 909 3.756963 CGAATCATCCGACTGATACCCTA 59.243 47.826 0.88 0.00 34.79 3.53
861 930 3.498834 TGCATTGGCGCTGCTACG 61.499 61.111 19.22 0.28 45.35 3.51
873 942 2.671070 CTGGACCCCTCGTGCATT 59.329 61.111 0.00 0.00 42.55 3.56
1000 1553 0.445436 CGTTTGATCTGGCTGCTGAC 59.555 55.000 0.00 0.00 0.00 3.51
1019 1572 0.035739 TCACGAACCAAACCCTAGGC 59.964 55.000 2.05 0.00 0.00 3.93
1158 1711 2.044352 TCGATGGAGCCGGTGAGA 60.044 61.111 1.90 0.00 0.00 3.27
1386 1939 1.633432 CATACCTTGGGGTGGAACTGA 59.367 52.381 0.00 0.00 46.75 3.41
1463 2016 4.219115 TCTCTCAGTCACTCAACCTCTTT 58.781 43.478 0.00 0.00 0.00 2.52
1641 2195 5.128499 TGAAAGAAGCCCACAAATTTCTTCA 59.872 36.000 15.17 0.00 38.54 3.02
1860 2422 2.103263 ACCTCTCCCGCTACATGATTTC 59.897 50.000 0.00 0.00 0.00 2.17
1893 2455 3.366374 GCACCACACTGCTTTCCTAAATC 60.366 47.826 0.00 0.00 34.06 2.17
2010 2572 1.400242 CGCTTGCAGCCTCTAACAAAC 60.400 52.381 0.00 0.00 38.18 2.93
2013 2575 0.950555 CACGCTTGCAGCCTCTAACA 60.951 55.000 0.00 0.00 38.18 2.41
2065 2627 8.718102 ACAACATAAACTTCATAGCGTAGAAT 57.282 30.769 0.00 0.00 0.00 2.40
2094 2656 5.881443 AGTCGTCTAGAAAGCATAGTACAGT 59.119 40.000 0.00 0.00 0.00 3.55
2095 2657 6.366315 AGTCGTCTAGAAAGCATAGTACAG 57.634 41.667 0.00 0.00 0.00 2.74
2096 2658 9.722184 ATATAGTCGTCTAGAAAGCATAGTACA 57.278 33.333 0.00 0.00 0.00 2.90
2162 2786 8.795899 TCCAATCATGATTAATTTAACCCCAT 57.204 30.769 20.32 0.00 0.00 4.00
2208 2832 1.359130 AGCTTAGTGAGGCCCCAAAAT 59.641 47.619 0.00 0.00 0.00 1.82
2279 2903 7.219484 ACAGCTTACTTCAGCACATTATTTT 57.781 32.000 0.00 0.00 42.84 1.82
2291 2915 2.902705 ACGGACAACAGCTTACTTCA 57.097 45.000 0.00 0.00 0.00 3.02
2324 2948 8.931385 AACAATGTGATTCATATTAACAAGGC 57.069 30.769 8.14 0.00 35.48 4.35
2332 2956 9.773328 CGTGAAAGTAACAATGTGATTCATATT 57.227 29.630 3.06 3.06 35.48 1.28
2333 2957 9.161629 TCGTGAAAGTAACAATGTGATTCATAT 57.838 29.630 6.66 0.00 35.48 1.78
2504 3128 9.926158 TGCATGTGTCAGAACATATTAAAATTT 57.074 25.926 0.00 0.00 38.75 1.82
2507 3131 8.738106 TCATGCATGTGTCAGAACATATTAAAA 58.262 29.630 25.43 0.00 38.75 1.52
2523 3147 9.649167 TCAATCTAGTTATAGATCATGCATGTG 57.351 33.333 25.43 10.90 46.08 3.21
2540 3164 7.701539 TGCAATAAAACCATGTCAATCTAGT 57.298 32.000 0.00 0.00 0.00 2.57
2545 3169 7.718272 GCATATGCAATAAAACCATGTCAAT 57.282 32.000 22.84 0.00 41.59 2.57
2562 3186 6.963242 CACCAAAATATATCGACTGCATATGC 59.037 38.462 21.09 21.09 42.50 3.14
2590 3214 7.394359 ACACAAGACTCAAGCAATAACCATTAT 59.606 33.333 0.00 0.00 0.00 1.28
2593 3217 5.048504 CACACAAGACTCAAGCAATAACCAT 60.049 40.000 0.00 0.00 0.00 3.55
2599 3223 4.454847 CAGATCACACAAGACTCAAGCAAT 59.545 41.667 0.00 0.00 0.00 3.56
2613 3237 3.511699 TGATTACGCTGTCAGATCACAC 58.488 45.455 3.32 0.00 0.00 3.82
2677 3301 4.638421 GCTAATTGGTTACAGTGCCATACA 59.362 41.667 0.00 0.00 34.37 2.29
2717 3341 3.006752 GGGCAATTCATTCACAGGTTTCA 59.993 43.478 0.00 0.00 0.00 2.69
2731 3355 7.484959 CGTAAATCAGAAAAACTAGGGCAATTC 59.515 37.037 0.00 0.00 0.00 2.17
2741 3365 6.488683 TGATTCCACCGTAAATCAGAAAAACT 59.511 34.615 4.98 0.00 37.06 2.66
2752 3376 3.322541 TGACAGACTGATTCCACCGTAAA 59.677 43.478 10.08 0.00 0.00 2.01
2767 3391 8.556194 TGACAAAGTGTATACAAATTGACAGAC 58.444 33.333 26.50 16.41 31.04 3.51
2789 3413 7.012894 CCTGTTAATAACTCAACCTGTTTGACA 59.987 37.037 4.67 0.00 39.45 3.58
2790 3414 7.012989 ACCTGTTAATAACTCAACCTGTTTGAC 59.987 37.037 4.67 0.00 39.45 3.18
2791 3415 7.012894 CACCTGTTAATAACTCAACCTGTTTGA 59.987 37.037 4.67 0.00 42.26 2.69
2792 3416 7.012894 TCACCTGTTAATAACTCAACCTGTTTG 59.987 37.037 4.67 0.00 36.42 2.93
2795 3419 6.182507 TCACCTGTTAATAACTCAACCTGT 57.817 37.500 4.67 0.00 0.00 4.00
2796 3420 7.390440 TCATTCACCTGTTAATAACTCAACCTG 59.610 37.037 4.67 0.00 0.00 4.00
2797 3421 7.458397 TCATTCACCTGTTAATAACTCAACCT 58.542 34.615 4.67 0.00 0.00 3.50
2798 3422 7.681939 TCATTCACCTGTTAATAACTCAACC 57.318 36.000 4.67 0.00 0.00 3.77
2801 3425 9.513906 TCATTTCATTCACCTGTTAATAACTCA 57.486 29.630 4.67 0.00 0.00 3.41
2807 3431 9.039165 AGGAAATCATTTCATTCACCTGTTAAT 57.961 29.630 12.27 0.00 41.43 1.40
2808 3432 8.421249 AGGAAATCATTTCATTCACCTGTTAA 57.579 30.769 12.27 0.00 41.43 2.01
2815 3439 7.807687 CTGACAAGGAAATCATTTCATTCAC 57.192 36.000 12.27 7.71 41.19 3.18
3139 3763 0.320683 CACATCCGGTCAAGAGCACA 60.321 55.000 0.00 0.00 0.00 4.57
3178 3802 1.417890 CCCTTCTCCTTGGCATCGTAT 59.582 52.381 0.00 0.00 0.00 3.06
3532 4156 2.282820 GCTTTAGTCAGCATCGTACAGC 59.717 50.000 0.00 0.00 39.83 4.40
3556 4180 1.165907 CCCGCTCAACTTGCAAGTGA 61.166 55.000 31.73 25.92 39.66 3.41
3637 4262 1.880271 CAGAGACGAGCTATACCCGA 58.120 55.000 0.00 0.00 0.00 5.14
3717 4473 5.817816 AGCAGATAAGTACTAACATGTTGGC 59.182 40.000 21.42 6.41 0.00 4.52
3723 4479 5.661458 ACGCAAGCAGATAAGTACTAACAT 58.339 37.500 0.00 0.00 45.62 2.71
3725 4481 5.220416 CCAACGCAAGCAGATAAGTACTAAC 60.220 44.000 0.00 0.00 45.62 2.34
3726 4482 4.868171 CCAACGCAAGCAGATAAGTACTAA 59.132 41.667 0.00 0.00 45.62 2.24
3727 4483 4.158949 TCCAACGCAAGCAGATAAGTACTA 59.841 41.667 0.00 0.00 45.62 1.82
3728 4484 3.056107 TCCAACGCAAGCAGATAAGTACT 60.056 43.478 0.00 0.00 45.62 2.73
3729 4485 3.062234 GTCCAACGCAAGCAGATAAGTAC 59.938 47.826 0.00 0.00 45.62 2.73
3735 4519 1.580845 GCAGTCCAACGCAAGCAGAT 61.581 55.000 0.00 0.00 45.62 2.90
3855 4639 7.630242 TTGAAAATCAGGGTATTGAGACATC 57.370 36.000 0.00 0.00 0.00 3.06
3856 4640 7.417116 GCATTGAAAATCAGGGTATTGAGACAT 60.417 37.037 0.00 0.00 0.00 3.06
3857 4641 6.127647 GCATTGAAAATCAGGGTATTGAGACA 60.128 38.462 0.00 0.00 0.00 3.41
3858 4642 6.268566 GCATTGAAAATCAGGGTATTGAGAC 58.731 40.000 0.00 0.00 0.00 3.36
3859 4643 5.360714 GGCATTGAAAATCAGGGTATTGAGA 59.639 40.000 0.00 0.00 0.00 3.27
3862 4646 5.341872 TGGCATTGAAAATCAGGGTATTG 57.658 39.130 0.00 0.00 0.00 1.90
3863 4647 7.860649 ATATGGCATTGAAAATCAGGGTATT 57.139 32.000 4.78 0.00 0.00 1.89
3866 4936 7.860649 ATTATATGGCATTGAAAATCAGGGT 57.139 32.000 4.78 0.00 0.00 4.34
3881 4951 1.128692 GCGTCCGCTGAATTATATGGC 59.871 52.381 4.10 0.00 38.26 4.40
3912 4982 1.633432 TCCGACCCAAACATCATCCTT 59.367 47.619 0.00 0.00 0.00 3.36
3919 4989 0.970427 GGCCAATCCGACCCAAACAT 60.970 55.000 0.00 0.00 0.00 2.71
3944 5014 2.677524 TGCCATCCAACAGCTGCC 60.678 61.111 15.27 0.00 0.00 4.85
3949 5019 2.562912 GCACGTGCCATCCAACAG 59.437 61.111 30.12 0.00 34.31 3.16
3971 5041 2.651361 CGGCAGAGAACAGACGGT 59.349 61.111 0.00 0.00 30.42 4.83
3977 5047 2.664851 CAACGCCGGCAGAGAACA 60.665 61.111 28.98 0.00 0.00 3.18
3979 5049 2.357034 GTCAACGCCGGCAGAGAA 60.357 61.111 28.98 4.09 0.00 2.87
4027 5097 0.936297 CGTGTTGCAAAGCCTCAAGC 60.936 55.000 0.00 0.00 44.25 4.01
4030 5100 1.785041 GCTCGTGTTGCAAAGCCTCA 61.785 55.000 9.29 0.00 0.00 3.86
4032 5102 1.526917 AGCTCGTGTTGCAAAGCCT 60.527 52.632 15.50 2.97 35.32 4.58
4049 5119 3.357079 GGACGGGCAGCAACACAG 61.357 66.667 0.00 0.00 0.00 3.66
4057 5127 1.597797 ATGTTGCAATGGACGGGCAG 61.598 55.000 0.59 0.00 38.97 4.85
4063 5133 1.473258 TGGGCTATGTTGCAATGGAC 58.527 50.000 0.59 0.00 34.04 4.02
4064 5134 2.033372 CATGGGCTATGTTGCAATGGA 58.967 47.619 0.59 0.00 34.04 3.41
4083 5187 2.481289 TGTCCATATTGTCCGCAACA 57.519 45.000 0.00 0.00 37.44 3.33
4110 5214 0.969894 GGGGACGATGCTAGCACTAT 59.030 55.000 22.07 7.96 0.00 2.12
4111 5215 0.106167 AGGGGACGATGCTAGCACTA 60.106 55.000 22.07 0.00 0.00 2.74
4130 5234 3.304391 GCTGCAAGGTTTTCATCAACGTA 60.304 43.478 0.00 0.00 0.00 3.57
4138 5242 0.459489 GTGGTGCTGCAAGGTTTTCA 59.541 50.000 2.77 0.00 0.00 2.69
4159 5266 4.906792 GCTGCTGCGAGGCCTAGG 62.907 72.222 15.29 3.67 0.00 3.02
4200 5307 3.480133 CTACAGGGGAAGGCGGGG 61.480 72.222 0.00 0.00 0.00 5.73
4208 5315 0.905357 GAGAGCTTTGCTACAGGGGA 59.095 55.000 0.00 0.00 39.88 4.81
4211 5318 0.532573 TCCGAGAGCTTTGCTACAGG 59.467 55.000 0.00 0.00 39.88 4.00
4260 5367 3.474570 CCCAGGGGCTCTCCTTCG 61.475 72.222 0.00 0.00 34.31 3.79
4262 5369 2.612115 CACCCAGGGGCTCTCCTT 60.612 66.667 11.37 0.00 39.32 3.36
4263 5370 2.713111 TTTCACCCAGGGGCTCTCCT 62.713 60.000 11.37 0.00 39.32 3.69
4266 5373 2.539081 GGTTTCACCCAGGGGCTCT 61.539 63.158 11.37 0.00 39.32 4.09
4267 5374 2.035783 GGTTTCACCCAGGGGCTC 59.964 66.667 11.37 0.00 39.32 4.70
4277 5384 1.376812 CTACGGCAGGGGGTTTCAC 60.377 63.158 0.00 0.00 0.00 3.18
4278 5385 2.598787 CCTACGGCAGGGGGTTTCA 61.599 63.158 0.00 0.00 41.26 2.69
4279 5386 2.271173 CCTACGGCAGGGGGTTTC 59.729 66.667 0.00 0.00 41.26 2.78
4287 5394 4.514577 CACGCTCCCCTACGGCAG 62.515 72.222 0.00 0.00 0.00 4.85
4289 5396 4.208686 CTCACGCTCCCCTACGGC 62.209 72.222 0.00 0.00 0.00 5.68
4290 5397 3.528370 CCTCACGCTCCCCTACGG 61.528 72.222 0.00 0.00 0.00 4.02
4291 5398 2.439701 TCCTCACGCTCCCCTACG 60.440 66.667 0.00 0.00 0.00 3.51
4292 5399 1.043673 ATGTCCTCACGCTCCCCTAC 61.044 60.000 0.00 0.00 0.00 3.18
4293 5400 1.043116 CATGTCCTCACGCTCCCCTA 61.043 60.000 0.00 0.00 0.00 3.53
4294 5401 2.039624 ATGTCCTCACGCTCCCCT 59.960 61.111 0.00 0.00 0.00 4.79
4295 5402 2.187946 CATGTCCTCACGCTCCCC 59.812 66.667 0.00 0.00 0.00 4.81
4296 5403 1.142748 CTCATGTCCTCACGCTCCC 59.857 63.158 0.00 0.00 0.00 4.30
4297 5404 1.520342 GCTCATGTCCTCACGCTCC 60.520 63.158 0.00 0.00 0.00 4.70
4298 5405 0.805322 CTGCTCATGTCCTCACGCTC 60.805 60.000 0.00 0.00 0.00 5.03
4299 5406 1.217511 CTGCTCATGTCCTCACGCT 59.782 57.895 0.00 0.00 0.00 5.07
4300 5407 2.459442 GCTGCTCATGTCCTCACGC 61.459 63.158 0.00 0.00 0.00 5.34
4301 5408 1.812922 GGCTGCTCATGTCCTCACG 60.813 63.158 0.00 0.00 0.00 4.35
4302 5409 1.812922 CGGCTGCTCATGTCCTCAC 60.813 63.158 0.00 0.00 0.00 3.51
4303 5410 2.580815 CGGCTGCTCATGTCCTCA 59.419 61.111 0.00 0.00 0.00 3.86
4304 5411 2.894387 GCGGCTGCTCATGTCCTC 60.894 66.667 11.21 0.00 38.39 3.71
4305 5412 4.479993 GGCGGCTGCTCATGTCCT 62.480 66.667 18.85 0.00 42.25 3.85
4306 5413 4.479993 AGGCGGCTGCTCATGTCC 62.480 66.667 18.85 0.00 42.25 4.02
4307 5414 3.200593 CAGGCGGCTGCTCATGTC 61.201 66.667 27.04 0.00 42.25 3.06
4315 5422 2.359850 TACTTTGGCAGGCGGCTG 60.360 61.111 32.81 32.81 44.01 4.85
4316 5423 2.045926 CTACTTTGGCAGGCGGCT 60.046 61.111 5.25 5.25 44.01 5.52
4317 5424 3.134127 CCTACTTTGGCAGGCGGC 61.134 66.667 0.00 0.00 43.74 6.53
4318 5425 1.450312 CTCCTACTTTGGCAGGCGG 60.450 63.158 0.00 0.00 0.00 6.13
4319 5426 0.460987 CTCTCCTACTTTGGCAGGCG 60.461 60.000 0.00 0.00 0.00 5.52
4320 5427 0.905357 TCTCTCCTACTTTGGCAGGC 59.095 55.000 0.00 0.00 0.00 4.85
4321 5428 3.703001 TTTCTCTCCTACTTTGGCAGG 57.297 47.619 0.00 0.00 0.00 4.85
4322 5429 4.083057 GCTTTTTCTCTCCTACTTTGGCAG 60.083 45.833 0.00 0.00 0.00 4.85
4323 5430 3.821033 GCTTTTTCTCTCCTACTTTGGCA 59.179 43.478 0.00 0.00 0.00 4.92
4324 5431 3.120165 CGCTTTTTCTCTCCTACTTTGGC 60.120 47.826 0.00 0.00 0.00 4.52
4325 5432 4.315803 TCGCTTTTTCTCTCCTACTTTGG 58.684 43.478 0.00 0.00 0.00 3.28
4326 5433 5.106908 CCTTCGCTTTTTCTCTCCTACTTTG 60.107 44.000 0.00 0.00 0.00 2.77
4327 5434 4.998033 CCTTCGCTTTTTCTCTCCTACTTT 59.002 41.667 0.00 0.00 0.00 2.66
4328 5435 4.563786 CCCTTCGCTTTTTCTCTCCTACTT 60.564 45.833 0.00 0.00 0.00 2.24
4329 5436 3.055747 CCCTTCGCTTTTTCTCTCCTACT 60.056 47.826 0.00 0.00 0.00 2.57
4330 5437 3.263261 CCCTTCGCTTTTTCTCTCCTAC 58.737 50.000 0.00 0.00 0.00 3.18
4331 5438 2.236395 CCCCTTCGCTTTTTCTCTCCTA 59.764 50.000 0.00 0.00 0.00 2.94
4332 5439 1.003696 CCCCTTCGCTTTTTCTCTCCT 59.996 52.381 0.00 0.00 0.00 3.69
4333 5440 1.003233 TCCCCTTCGCTTTTTCTCTCC 59.997 52.381 0.00 0.00 0.00 3.71
4334 5441 2.351455 CTCCCCTTCGCTTTTTCTCTC 58.649 52.381 0.00 0.00 0.00 3.20
4335 5442 1.003696 CCTCCCCTTCGCTTTTTCTCT 59.996 52.381 0.00 0.00 0.00 3.10
4336 5443 1.003233 TCCTCCCCTTCGCTTTTTCTC 59.997 52.381 0.00 0.00 0.00 2.87
4337 5444 1.064825 TCCTCCCCTTCGCTTTTTCT 58.935 50.000 0.00 0.00 0.00 2.52
4338 5445 1.166129 GTCCTCCCCTTCGCTTTTTC 58.834 55.000 0.00 0.00 0.00 2.29
4339 5446 0.476771 TGTCCTCCCCTTCGCTTTTT 59.523 50.000 0.00 0.00 0.00 1.94
4340 5447 0.698818 ATGTCCTCCCCTTCGCTTTT 59.301 50.000 0.00 0.00 0.00 2.27
4341 5448 0.035056 CATGTCCTCCCCTTCGCTTT 60.035 55.000 0.00 0.00 0.00 3.51
4342 5449 0.909610 TCATGTCCTCCCCTTCGCTT 60.910 55.000 0.00 0.00 0.00 4.68
4343 5450 1.306141 TCATGTCCTCCCCTTCGCT 60.306 57.895 0.00 0.00 0.00 4.93
4344 5451 1.144936 CTCATGTCCTCCCCTTCGC 59.855 63.158 0.00 0.00 0.00 4.70
4345 5452 1.144936 GCTCATGTCCTCCCCTTCG 59.855 63.158 0.00 0.00 0.00 3.79
4346 5453 0.179936 CTGCTCATGTCCTCCCCTTC 59.820 60.000 0.00 0.00 0.00 3.46
4347 5454 1.919600 GCTGCTCATGTCCTCCCCTT 61.920 60.000 0.00 0.00 0.00 3.95
4348 5455 2.373707 GCTGCTCATGTCCTCCCCT 61.374 63.158 0.00 0.00 0.00 4.79
4349 5456 2.191641 GCTGCTCATGTCCTCCCC 59.808 66.667 0.00 0.00 0.00 4.81
4350 5457 2.191641 GGCTGCTCATGTCCTCCC 59.808 66.667 0.00 0.00 0.00 4.30
4351 5458 2.202987 CGGCTGCTCATGTCCTCC 60.203 66.667 0.00 0.00 0.00 4.30
4352 5459 2.894387 GCGGCTGCTCATGTCCTC 60.894 66.667 11.21 0.00 38.39 3.71
4353 5460 4.479993 GGCGGCTGCTCATGTCCT 62.480 66.667 18.85 0.00 42.25 3.85
4354 5461 4.479993 AGGCGGCTGCTCATGTCC 62.480 66.667 18.85 0.00 42.25 4.02
4355 5462 3.200593 CAGGCGGCTGCTCATGTC 61.201 66.667 27.04 0.00 42.25 3.06
4363 5470 2.359850 TACTTTGGCAGGCGGCTG 60.360 61.111 32.81 32.81 44.01 4.85
4364 5471 2.045926 CTACTTTGGCAGGCGGCT 60.046 61.111 5.25 5.25 44.01 5.52
4365 5472 3.134127 CCTACTTTGGCAGGCGGC 61.134 66.667 0.00 0.00 43.74 6.53
4366 5473 1.450312 CTCCTACTTTGGCAGGCGG 60.450 63.158 0.00 0.00 0.00 6.13
4367 5474 0.460987 CTCTCCTACTTTGGCAGGCG 60.461 60.000 0.00 0.00 0.00 5.52
4379 5486 1.831736 CCCCTTCGCTTTTCTCTCCTA 59.168 52.381 0.00 0.00 0.00 2.94
4381 5488 0.613777 TCCCCTTCGCTTTTCTCTCC 59.386 55.000 0.00 0.00 0.00 3.71
4439 5546 1.235281 GGTGGGCAGACGAGGAAAAC 61.235 60.000 0.00 0.00 0.00 2.43
4484 5591 1.009449 CGAGCCGTCGGATCTCTTC 60.009 63.158 25.73 1.40 42.87 2.87
4524 5631 6.280855 TCTCTATTTCAACCGACTGATTGA 57.719 37.500 0.00 0.00 33.03 2.57


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

AutoCloner maintained by Alex Coulton.