Multiple sequence alignment - TraesCS2D01G532700

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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 TraesCS2D01G532700 chr2D 100.000 3661 0 0 1 3661 617889854 617893514 0.000000e+00 6761
1 TraesCS2D01G532700 chr2D 100.000 1679 0 0 3946 5624 617893799 617895477 0.000000e+00 3101
2 TraesCS2D01G532700 chr2D 84.829 468 45 10 2 454 617549001 617549457 1.110000e-121 448
3 TraesCS2D01G532700 chr2D 85.761 309 23 7 1 290 617733430 617733736 1.970000e-79 307
4 TraesCS2D01G532700 chr2D 87.162 148 8 5 751 894 617549603 617549743 2.100000e-34 158
5 TraesCS2D01G532700 chr2A 95.105 2676 92 19 998 3659 748441083 748443733 0.000000e+00 4180
6 TraesCS2D01G532700 chr2A 91.819 1699 57 21 3946 5624 748443753 748445389 0.000000e+00 2292
7 TraesCS2D01G532700 chr2A 95.331 514 12 3 1 513 748440102 748440604 0.000000e+00 806
8 TraesCS2D01G532700 chr2A 83.817 482 44 16 1 457 748402486 748402958 1.450000e-115 427
9 TraesCS2D01G532700 chr2A 91.176 306 25 2 514 817 748440642 748440947 1.130000e-111 414
10 TraesCS2D01G532700 chr2A 86.486 148 9 4 751 894 748416349 748416489 9.760000e-33 152
11 TraesCS2D01G532700 chr2B 95.179 1701 44 12 3951 5624 753802252 753800563 0.000000e+00 2652
12 TraesCS2D01G532700 chr2B 92.828 1241 35 26 943 2165 753805206 753804002 0.000000e+00 1749
13 TraesCS2D01G532700 chr2B 98.538 889 11 2 2751 3639 753803437 753802551 0.000000e+00 1568
14 TraesCS2D01G532700 chr2B 95.833 408 17 0 2164 2571 753803840 753803433 0.000000e+00 660
15 TraesCS2D01G532700 chr2B 87.984 258 20 5 1 253 753806089 753805838 1.530000e-75 294
16 TraesCS2D01G532700 chr2B 82.540 189 16 10 328 516 753805834 753805663 3.510000e-32 150
17 TraesCS2D01G532700 chr6A 95.129 657 19 5 4420 5073 477475573 477476219 0.000000e+00 1024
18 TraesCS2D01G532700 chr6A 94.673 657 23 6 4420 5073 239256593 239255946 0.000000e+00 1009
19 TraesCS2D01G532700 chr7B 94.825 657 21 5 4420 5073 382088094 382087448 0.000000e+00 1013
20 TraesCS2D01G532700 chr7B 89.474 494 44 7 5134 5620 745144748 745144256 8.010000e-173 617
21 TraesCS2D01G532700 chr7B 87.248 298 27 6 1 293 7811048 7810757 4.200000e-86 329
22 TraesCS2D01G532700 chr6B 94.825 657 21 5 4420 5073 714156442 714157088 0.000000e+00 1013
23 TraesCS2D01G532700 chr6B 94.521 657 23 5 4420 5073 40510416 40509770 0.000000e+00 1002
24 TraesCS2D01G532700 chr4A 94.673 657 22 5 4420 5073 29478217 29478863 0.000000e+00 1007
25 TraesCS2D01G532700 chr4A 94.521 657 23 5 4420 5073 51046773 51046127 0.000000e+00 1002
26 TraesCS2D01G532700 chr1B 94.673 657 22 5 4420 5073 82987588 82988234 0.000000e+00 1007
27 TraesCS2D01G532700 chr7D 88.889 495 41 7 5134 5624 632163997 632163513 1.040000e-166 597
28 TraesCS2D01G532700 chr1A 89.024 492 40 8 5134 5624 6422214 6422692 1.040000e-166 597
29 TraesCS2D01G532700 chr5D 90.681 279 24 2 1263 1540 451684363 451684640 2.470000e-98 370
30 TraesCS2D01G532700 chr5B 90.036 281 26 2 1261 1540 551509137 551509416 4.140000e-96 363


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 TraesCS2D01G532700 chr2D 617889854 617895477 5623 False 4931.000000 6761 100.000000 1 5624 2 chr2D.!!$F3 5623
1 TraesCS2D01G532700 chr2D 617549001 617549743 742 False 303.000000 448 85.995500 2 894 2 chr2D.!!$F2 892
2 TraesCS2D01G532700 chr2A 748440102 748445389 5287 False 1923.000000 4180 93.357750 1 5624 4 chr2A.!!$F3 5623
3 TraesCS2D01G532700 chr2B 753800563 753806089 5526 True 1178.833333 2652 92.150333 1 5624 6 chr2B.!!$R1 5623
4 TraesCS2D01G532700 chr6A 477475573 477476219 646 False 1024.000000 1024 95.129000 4420 5073 1 chr6A.!!$F1 653
5 TraesCS2D01G532700 chr6A 239255946 239256593 647 True 1009.000000 1009 94.673000 4420 5073 1 chr6A.!!$R1 653
6 TraesCS2D01G532700 chr7B 382087448 382088094 646 True 1013.000000 1013 94.825000 4420 5073 1 chr7B.!!$R2 653
7 TraesCS2D01G532700 chr6B 714156442 714157088 646 False 1013.000000 1013 94.825000 4420 5073 1 chr6B.!!$F1 653
8 TraesCS2D01G532700 chr6B 40509770 40510416 646 True 1002.000000 1002 94.521000 4420 5073 1 chr6B.!!$R1 653
9 TraesCS2D01G532700 chr4A 29478217 29478863 646 False 1007.000000 1007 94.673000 4420 5073 1 chr4A.!!$F1 653
10 TraesCS2D01G532700 chr4A 51046127 51046773 646 True 1002.000000 1002 94.521000 4420 5073 1 chr4A.!!$R1 653
11 TraesCS2D01G532700 chr1B 82987588 82988234 646 False 1007.000000 1007 94.673000 4420 5073 1 chr1B.!!$F1 653

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
629 683 0.108329 ACTACTGCCGTTGGGATTCG 60.108 55.000 0.00 0.0 34.06 3.34 F
919 978 0.196118 TCCTTCCCTTCCTTCCCTGT 59.804 55.000 0.00 0.0 0.00 4.00 F
920 979 0.329596 CCTTCCCTTCCTTCCCTGTG 59.670 60.000 0.00 0.0 0.00 3.66 F
939 1027 0.764752 GATGAGGTAGGGAGTGGGGG 60.765 65.000 0.00 0.0 0.00 5.40 F
2047 2399 0.108804 TGTTCGAGCGTCTTGGGATC 60.109 55.000 0.00 0.0 0.00 3.36 F
3160 3677 1.350019 GGGCTGTACTGTGGTACCTTT 59.650 52.381 14.36 0.0 45.49 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 1859 1.005037 TTGCTTGATGACGAGGCGT 60.005 52.632 0.00 0.0 45.10 5.68 R
1924 2276 1.402968 CAAGGTGAATCAGAATGGGCG 59.597 52.381 0.00 0.0 36.16 6.13 R
2047 2399 1.447838 CCCCACATCCGAAGACGTG 60.448 63.158 0.00 0.0 37.88 4.49 R
2625 3141 2.673368 GGATAAACAGCACGAAGTCCAG 59.327 50.000 0.00 0.0 41.61 3.86 R
3282 3799 1.133976 AGCACCTCTGCATGGGAATAC 60.134 52.381 11.38 0.0 46.97 1.89 R
5111 5663 2.731976 GTGACGCCAACAAAACAAAACA 59.268 40.909 0.00 0.0 0.00 2.83 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
184 190 5.880332 TGTGATATTTTTCAGTAGTGCCTCC 59.120 40.000 0.00 0.00 0.00 4.30
200 206 2.224548 GCCTCCCTCAACAGTAGTGTTT 60.225 50.000 13.37 0.00 45.00 2.83
290 296 9.467258 AATTGAACTGTGTTGTCATCTAAAATG 57.533 29.630 0.00 0.00 0.00 2.32
392 408 4.222114 GCAACTGCTGACTGTCAAAATAC 58.778 43.478 12.16 0.44 38.21 1.89
508 525 1.996191 GACGAACAGAGCATGAAGGAC 59.004 52.381 0.00 0.00 0.00 3.85
555 609 6.877611 TGTCTATGTTTCTTTTTCCTGGTC 57.122 37.500 0.00 0.00 0.00 4.02
581 635 4.158394 GCTAGAGCTATCAGAGGGAAGATG 59.842 50.000 0.00 0.00 38.21 2.90
585 639 3.116784 AGCTATCAGAGGGAAGATGGAGT 60.117 47.826 0.00 0.00 0.00 3.85
595 649 2.419297 GGAAGATGGAGTGAGCGTGAAT 60.419 50.000 0.00 0.00 0.00 2.57
629 683 0.108329 ACTACTGCCGTTGGGATTCG 60.108 55.000 0.00 0.00 34.06 3.34
646 700 2.198827 TCGCATCCCAGAAACATGTT 57.801 45.000 4.92 4.92 0.00 2.71
648 702 1.733389 CGCATCCCAGAAACATGTTGC 60.733 52.381 12.82 10.70 0.00 4.17
698 752 6.445357 TTGTTGTTAAGGTTCTCCAGTTTC 57.555 37.500 0.00 0.00 35.89 2.78
699 753 5.751586 TGTTGTTAAGGTTCTCCAGTTTCT 58.248 37.500 0.00 0.00 35.89 2.52
703 757 7.712204 TGTTAAGGTTCTCCAGTTTCTTTTT 57.288 32.000 0.00 0.00 35.89 1.94
715 770 5.811613 CCAGTTTCTTTTTGTTGCTGATGAA 59.188 36.000 0.00 0.00 0.00 2.57
718 773 6.536224 AGTTTCTTTTTGTTGCTGATGAAAGG 59.464 34.615 0.00 0.00 0.00 3.11
743 798 3.311966 GAAAGCCATTTCTTGTGTGCTC 58.688 45.455 0.00 0.00 41.41 4.26
837 892 4.348495 AGCGGAAGGGGAAGGGGA 62.348 66.667 0.00 0.00 0.00 4.81
855 910 4.796408 AGGAGCTTCCTCGTCCAT 57.204 55.556 0.00 0.00 45.66 3.41
866 921 4.429212 CGTCCATGACCACGCCGA 62.429 66.667 0.00 0.00 0.00 5.54
900 959 2.029828 GTCACATTGACTGACGACCTCT 60.030 50.000 0.00 0.00 43.73 3.69
911 970 0.615261 ACGACCTCTCCTTCCCTTCC 60.615 60.000 0.00 0.00 0.00 3.46
913 972 1.897647 CGACCTCTCCTTCCCTTCCTT 60.898 57.143 0.00 0.00 0.00 3.36
915 974 1.208706 CCTCTCCTTCCCTTCCTTCC 58.791 60.000 0.00 0.00 0.00 3.46
916 975 1.208706 CTCTCCTTCCCTTCCTTCCC 58.791 60.000 0.00 0.00 0.00 3.97
918 977 0.915364 CTCCTTCCCTTCCTTCCCTG 59.085 60.000 0.00 0.00 0.00 4.45
919 978 0.196118 TCCTTCCCTTCCTTCCCTGT 59.804 55.000 0.00 0.00 0.00 4.00
920 979 0.329596 CCTTCCCTTCCTTCCCTGTG 59.670 60.000 0.00 0.00 0.00 3.66
921 980 1.362224 CTTCCCTTCCTTCCCTGTGA 58.638 55.000 0.00 0.00 0.00 3.58
923 982 1.289160 TCCCTTCCTTCCCTGTGATG 58.711 55.000 0.00 0.00 0.00 3.07
927 986 1.912043 CTTCCTTCCCTGTGATGAGGT 59.088 52.381 0.00 0.00 0.00 3.85
928 987 2.940514 TCCTTCCCTGTGATGAGGTA 57.059 50.000 0.00 0.00 0.00 3.08
929 988 2.752030 TCCTTCCCTGTGATGAGGTAG 58.248 52.381 0.00 0.00 0.00 3.18
934 993 2.166907 CCTGTGATGAGGTAGGGAGT 57.833 55.000 0.00 0.00 0.00 3.85
935 994 1.759445 CCTGTGATGAGGTAGGGAGTG 59.241 57.143 0.00 0.00 0.00 3.51
939 1027 0.764752 GATGAGGTAGGGAGTGGGGG 60.765 65.000 0.00 0.00 0.00 5.40
996 1316 1.826720 GCCTGGCCTTGAATGAATGAA 59.173 47.619 7.66 0.00 0.00 2.57
1055 1380 4.747605 GGAAGGAAGTTATCTCATCTTCGC 59.252 45.833 0.00 0.00 38.58 4.70
1081 1406 3.693572 AGCAGAGCTCCTCCCCCT 61.694 66.667 10.93 0.00 30.62 4.79
1515 1847 2.818132 CTCAGGCCGGAGATCACC 59.182 66.667 26.95 0.00 37.05 4.02
1527 1859 2.285368 ATCACCCCTTCCCTCGCA 60.285 61.111 0.00 0.00 0.00 5.10
1533 1865 4.821589 CCTTCCCTCGCACGCCTC 62.822 72.222 0.00 0.00 0.00 4.70
1559 1891 6.647067 GTCATCAAGCAAGGGTATGTATCTAC 59.353 42.308 0.00 0.00 0.00 2.59
1560 1892 6.554982 TCATCAAGCAAGGGTATGTATCTACT 59.445 38.462 0.00 0.00 0.00 2.57
1561 1893 6.406692 TCAAGCAAGGGTATGTATCTACTC 57.593 41.667 0.00 0.00 0.00 2.59
1562 1894 5.304614 TCAAGCAAGGGTATGTATCTACTCC 59.695 44.000 0.00 0.00 0.00 3.85
1564 1896 3.901844 GCAAGGGTATGTATCTACTCCCA 59.098 47.826 13.75 0.00 36.00 4.37
1581 1925 9.413734 TCTACTCCCATGTCTATGTATGATATG 57.586 37.037 0.00 0.00 34.32 1.78
1582 1926 9.413734 CTACTCCCATGTCTATGTATGATATGA 57.586 37.037 0.00 0.00 35.84 2.15
1583 1927 8.670521 ACTCCCATGTCTATGTATGATATGAA 57.329 34.615 0.00 0.00 35.84 2.57
1584 1928 9.276791 ACTCCCATGTCTATGTATGATATGAAT 57.723 33.333 0.00 0.00 35.84 2.57
1599 1943 8.818622 ATGATATGAATATGATTCAACCCAGG 57.181 34.615 6.01 0.00 31.55 4.45
1600 1944 7.758609 TGATATGAATATGATTCAACCCAGGT 58.241 34.615 6.01 0.00 31.55 4.00
1601 1945 8.889445 TGATATGAATATGATTCAACCCAGGTA 58.111 33.333 6.01 0.00 31.55 3.08
1602 1946 9.167311 GATATGAATATGATTCAACCCAGGTAC 57.833 37.037 6.01 0.00 31.55 3.34
1603 1947 6.575244 TGAATATGATTCAACCCAGGTACT 57.425 37.500 0.00 0.00 43.88 2.73
1604 1948 7.684317 TGAATATGATTCAACCCAGGTACTA 57.316 36.000 0.00 0.00 36.02 1.82
1605 1949 7.506114 TGAATATGATTCAACCCAGGTACTAC 58.494 38.462 0.00 0.00 36.02 2.73
1606 1950 7.347222 TGAATATGATTCAACCCAGGTACTACT 59.653 37.037 0.00 0.00 36.02 2.57
1607 1951 7.691993 ATATGATTCAACCCAGGTACTACTT 57.308 36.000 0.00 0.00 36.02 2.24
1644 1988 4.037089 TGGATGCCAATCTCAATTCATTCG 59.963 41.667 0.00 0.00 32.95 3.34
1711 2059 6.611613 AGATACCAGTCTCACTTCATTCAA 57.388 37.500 0.00 0.00 0.00 2.69
1750 2098 5.753438 CGCCTAGTAAGTGCATTTCTTCATA 59.247 40.000 0.00 0.00 0.00 2.15
1924 2276 6.830873 AAGTCCGGGTATGTATGTATCTAC 57.169 41.667 0.00 0.00 0.00 2.59
2047 2399 0.108804 TGTTCGAGCGTCTTGGGATC 60.109 55.000 0.00 0.00 0.00 3.36
2133 2486 7.878036 TGCCCTCTAATTACAAGTAAACAAAC 58.122 34.615 0.00 0.00 0.00 2.93
2153 2506 5.645056 AACCATTTTGTTCCCTTCCATTT 57.355 34.783 0.00 0.00 0.00 2.32
2320 2836 5.508200 TTGTTGACAAGGTACATCCAAAC 57.492 39.130 0.00 0.00 39.02 2.93
2325 2841 2.986728 ACAAGGTACATCCAAACCCTCT 59.013 45.455 0.00 0.00 36.34 3.69
2337 2853 1.834540 AACCCTCTTTCCACCTTCCT 58.165 50.000 0.00 0.00 0.00 3.36
2418 2934 3.635373 CAGCCATGGCATTCTGAATAACT 59.365 43.478 37.18 10.08 44.88 2.24
2505 3021 2.082231 CACCTCTTTCCACTGCTCATG 58.918 52.381 0.00 0.00 0.00 3.07
2510 3026 4.461781 CCTCTTTCCACTGCTCATGAAAAT 59.538 41.667 0.00 0.00 0.00 1.82
2636 3152 5.277825 TGTTTATTTTTGCTGGACTTCGTG 58.722 37.500 0.00 0.00 0.00 4.35
2664 3180 7.498900 TGTTTATCCTTTACTATGCAGTCCATG 59.501 37.037 0.00 0.00 36.14 3.66
2667 3183 6.553953 TCCTTTACTATGCAGTCCATGTAA 57.446 37.500 0.00 0.00 36.14 2.41
2669 3185 7.047891 TCCTTTACTATGCAGTCCATGTAAAG 58.952 38.462 18.40 18.40 43.70 1.85
2672 3188 9.764363 CTTTACTATGCAGTCCATGTAAAGATA 57.236 33.333 19.49 0.00 44.83 1.98
2681 3197 9.944376 GCAGTCCATGTAAAGATATAGGAAATA 57.056 33.333 0.00 0.00 0.00 1.40
2706 3222 6.161855 TCACTGAGTGTTCTTTGTATGACT 57.838 37.500 12.93 0.00 34.79 3.41
3160 3677 1.350019 GGGCTGTACTGTGGTACCTTT 59.650 52.381 14.36 0.00 45.49 3.11
3282 3799 4.418392 CAGAAAAGGATCGCTCATTTTGG 58.582 43.478 15.37 5.03 43.34 3.28
3659 4185 4.336889 TGCTGTTATAGTGGAGGTATGC 57.663 45.455 0.00 0.00 0.00 3.14
3660 4186 3.071023 TGCTGTTATAGTGGAGGTATGCC 59.929 47.826 0.00 0.00 0.00 4.40
4135 4661 7.965107 CCAAGATTTTATCAAGTTGAGTAGTGC 59.035 37.037 11.91 0.16 0.00 4.40
4184 4710 6.602179 AGATTGTCGTTGTTTACATGTCATG 58.398 36.000 11.41 11.41 0.00 3.07
4416 4942 5.296813 GACAAGCGTCTGAAATGGTAATT 57.703 39.130 0.00 0.00 39.22 1.40
4417 4943 5.699839 GACAAGCGTCTGAAATGGTAATTT 58.300 37.500 0.00 0.00 39.22 1.82
4753 5305 7.597386 GGCTTTAAAGGCTATTGATATCTTGG 58.403 38.462 29.08 0.00 46.98 3.61
4977 5529 2.170166 TGGAAATTAAGCTGGTGCCTG 58.830 47.619 0.00 0.00 40.80 4.85
5023 5575 3.379452 TGGGTTGGTCCTGAAAAACAAT 58.621 40.909 0.00 0.00 36.25 2.71
5034 5586 9.343539 GGTCCTGAAAAACAATAAGCTATCTAT 57.656 33.333 0.00 0.00 0.00 1.98
5107 5659 0.039527 GCCAGCAGGTACGGTTTTTG 60.040 55.000 0.00 0.00 37.19 2.44
5108 5660 1.314730 CCAGCAGGTACGGTTTTTGT 58.685 50.000 0.00 0.00 0.00 2.83
5111 5663 3.429684 CCAGCAGGTACGGTTTTTGTTTT 60.430 43.478 0.00 0.00 0.00 2.43
5112 5664 3.549873 CAGCAGGTACGGTTTTTGTTTTG 59.450 43.478 0.00 0.00 0.00 2.44
5113 5665 3.193903 AGCAGGTACGGTTTTTGTTTTGT 59.806 39.130 0.00 0.00 0.00 2.83
5209 5761 4.537751 TGAGGAGGTAGACATAGAAGTGG 58.462 47.826 0.00 0.00 0.00 4.00
5254 5806 2.889503 GCGCAGTAGAGCAGGCAG 60.890 66.667 0.30 0.00 40.58 4.85
5309 5861 3.120373 GCTTTGGCTCTTCTTCTTCTTCG 60.120 47.826 0.00 0.00 35.22 3.79
5365 5917 3.391382 GGGGTGGAGGAGGTCACG 61.391 72.222 0.00 0.00 34.93 4.35
5494 6046 2.029844 GAAGACGAGCAGGTGCCAC 61.030 63.158 0.00 0.00 43.38 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 183 0.977395 ACTACTGTTGAGGGAGGCAC 59.023 55.000 0.00 0.00 0.00 5.01
205 211 7.095397 GCACTTAACGCTTTCCCAAAATAAAAT 60.095 33.333 0.00 0.00 0.00 1.82
207 213 5.692654 GCACTTAACGCTTTCCCAAAATAAA 59.307 36.000 0.00 0.00 0.00 1.40
208 214 5.224135 GCACTTAACGCTTTCCCAAAATAA 58.776 37.500 0.00 0.00 0.00 1.40
209 215 4.614078 CGCACTTAACGCTTTCCCAAAATA 60.614 41.667 0.00 0.00 0.00 1.40
210 216 3.649073 GCACTTAACGCTTTCCCAAAAT 58.351 40.909 0.00 0.00 0.00 1.82
290 296 1.696832 GCACTAGCGCTGGCAACTAC 61.697 60.000 22.90 0.00 43.41 2.73
392 408 2.766263 TGGGGAGACTGCAATGTAGTAG 59.234 50.000 3.50 0.00 0.00 2.57
478 495 1.896465 CTCTGTTCGTCTCTCCCCTTT 59.104 52.381 0.00 0.00 0.00 3.11
528 582 7.092716 CCAGGAAAAAGAAACATAGACAATGG 58.907 38.462 0.00 0.00 40.16 3.16
576 630 2.234661 TCATTCACGCTCACTCCATCTT 59.765 45.455 0.00 0.00 0.00 2.40
581 635 2.200067 CTGATCATTCACGCTCACTCC 58.800 52.381 0.00 0.00 0.00 3.85
585 639 2.160219 GCAAACTGATCATTCACGCTCA 59.840 45.455 0.00 0.00 0.00 4.26
629 683 1.733389 CGCAACATGTTTCTGGGATGC 60.733 52.381 8.77 6.58 0.00 3.91
678 732 7.712204 AAAAGAAACTGGAGAACCTTAACAA 57.288 32.000 0.00 0.00 37.04 2.83
698 752 5.051508 CGTTCCTTTCATCAGCAACAAAAAG 60.052 40.000 0.00 0.00 0.00 2.27
699 753 4.803088 CGTTCCTTTCATCAGCAACAAAAA 59.197 37.500 0.00 0.00 0.00 1.94
703 757 2.844946 TCGTTCCTTTCATCAGCAACA 58.155 42.857 0.00 0.00 0.00 3.33
715 770 3.636764 ACAAGAAATGGCTTTCGTTCCTT 59.363 39.130 4.53 0.00 44.52 3.36
718 773 3.730715 CACACAAGAAATGGCTTTCGTTC 59.269 43.478 4.53 0.00 44.52 3.95
743 798 3.451526 ACTACGCACTCATCATGTCATG 58.548 45.455 6.47 6.47 0.00 3.07
821 876 3.335729 TTCCCCTTCCCCTTCCGC 61.336 66.667 0.00 0.00 0.00 5.54
822 877 2.680370 CCTTCCCCTTCCCCTTCCG 61.680 68.421 0.00 0.00 0.00 4.30
823 878 1.230182 TCCTTCCCCTTCCCCTTCC 60.230 63.158 0.00 0.00 0.00 3.46
824 879 1.927569 GCTCCTTCCCCTTCCCCTTC 61.928 65.000 0.00 0.00 0.00 3.46
825 880 1.931180 GCTCCTTCCCCTTCCCCTT 60.931 63.158 0.00 0.00 0.00 3.95
826 881 2.286502 GCTCCTTCCCCTTCCCCT 60.287 66.667 0.00 0.00 0.00 4.79
827 882 1.927569 GAAGCTCCTTCCCCTTCCCC 61.928 65.000 0.00 0.00 34.71 4.81
900 959 0.196118 ACAGGGAAGGAAGGGAAGGA 59.804 55.000 0.00 0.00 0.00 3.36
915 974 1.759445 CACTCCCTACCTCATCACAGG 59.241 57.143 0.00 0.00 39.80 4.00
916 975 1.759445 CCACTCCCTACCTCATCACAG 59.241 57.143 0.00 0.00 0.00 3.66
918 977 1.123928 CCCACTCCCTACCTCATCAC 58.876 60.000 0.00 0.00 0.00 3.06
919 978 0.031111 CCCCACTCCCTACCTCATCA 60.031 60.000 0.00 0.00 0.00 3.07
920 979 0.764752 CCCCCACTCCCTACCTCATC 60.765 65.000 0.00 0.00 0.00 2.92
921 980 1.318380 CCCCCACTCCCTACCTCAT 59.682 63.158 0.00 0.00 0.00 2.90
939 1027 0.951040 CGGTCCAGTTCAGTTCAGCC 60.951 60.000 0.00 0.00 0.00 4.85
986 1306 5.699458 GGCCCATTCATTCATTCATTCATTC 59.301 40.000 0.00 0.00 0.00 2.67
996 1316 0.846015 TCTCCGGCCCATTCATTCAT 59.154 50.000 0.00 0.00 0.00 2.57
1055 1380 3.459965 AGCTCTGCTCTGCCTCGG 61.460 66.667 0.00 0.00 30.62 4.63
1527 1859 1.005037 TTGCTTGATGACGAGGCGT 60.005 52.632 0.00 0.00 45.10 5.68
1533 1865 2.632377 ACATACCCTTGCTTGATGACG 58.368 47.619 0.00 0.00 0.00 4.35
1580 1924 6.575244 AGTACCTGGGTTGAATCATATTCA 57.425 37.500 0.00 0.00 0.00 2.57
1581 1925 7.736893 AGTAGTACCTGGGTTGAATCATATTC 58.263 38.462 0.00 0.00 0.00 1.75
1582 1926 7.691993 AGTAGTACCTGGGTTGAATCATATT 57.308 36.000 0.00 0.00 0.00 1.28
1583 1927 7.691993 AAGTAGTACCTGGGTTGAATCATAT 57.308 36.000 0.00 0.00 0.00 1.78
1584 1928 8.647796 CATAAGTAGTACCTGGGTTGAATCATA 58.352 37.037 0.00 0.00 0.00 2.15
1585 1929 7.347222 TCATAAGTAGTACCTGGGTTGAATCAT 59.653 37.037 0.00 0.00 0.00 2.45
1586 1930 6.670464 TCATAAGTAGTACCTGGGTTGAATCA 59.330 38.462 0.00 0.00 0.00 2.57
1587 1931 7.120923 TCATAAGTAGTACCTGGGTTGAATC 57.879 40.000 0.00 0.00 0.00 2.52
1588 1932 7.365652 CCTTCATAAGTAGTACCTGGGTTGAAT 60.366 40.741 0.00 0.00 0.00 2.57
1589 1933 6.070424 CCTTCATAAGTAGTACCTGGGTTGAA 60.070 42.308 0.00 0.00 0.00 2.69
1590 1934 5.424252 CCTTCATAAGTAGTACCTGGGTTGA 59.576 44.000 0.00 0.00 0.00 3.18
1591 1935 5.671493 CCTTCATAAGTAGTACCTGGGTTG 58.329 45.833 0.00 0.00 0.00 3.77
1592 1936 4.163649 GCCTTCATAAGTAGTACCTGGGTT 59.836 45.833 0.00 0.00 0.00 4.11
1593 1937 3.710165 GCCTTCATAAGTAGTACCTGGGT 59.290 47.826 0.00 0.00 0.00 4.51
1594 1938 3.967987 AGCCTTCATAAGTAGTACCTGGG 59.032 47.826 0.00 0.00 0.00 4.45
1595 1939 4.202264 CCAGCCTTCATAAGTAGTACCTGG 60.202 50.000 0.00 0.00 0.00 4.45
1596 1940 4.649674 TCCAGCCTTCATAAGTAGTACCTG 59.350 45.833 0.00 0.00 0.00 4.00
1597 1941 4.880164 TCCAGCCTTCATAAGTAGTACCT 58.120 43.478 0.00 0.00 0.00 3.08
1598 1942 5.810080 ATCCAGCCTTCATAAGTAGTACC 57.190 43.478 0.00 0.00 0.00 3.34
1599 1943 5.992217 CCAATCCAGCCTTCATAAGTAGTAC 59.008 44.000 0.00 0.00 0.00 2.73
1600 1944 5.903010 TCCAATCCAGCCTTCATAAGTAGTA 59.097 40.000 0.00 0.00 0.00 1.82
1601 1945 4.721776 TCCAATCCAGCCTTCATAAGTAGT 59.278 41.667 0.00 0.00 0.00 2.73
1602 1946 5.296151 TCCAATCCAGCCTTCATAAGTAG 57.704 43.478 0.00 0.00 0.00 2.57
1603 1947 5.624159 CATCCAATCCAGCCTTCATAAGTA 58.376 41.667 0.00 0.00 0.00 2.24
1604 1948 4.467769 CATCCAATCCAGCCTTCATAAGT 58.532 43.478 0.00 0.00 0.00 2.24
1605 1949 3.255149 GCATCCAATCCAGCCTTCATAAG 59.745 47.826 0.00 0.00 0.00 1.73
1606 1950 3.225104 GCATCCAATCCAGCCTTCATAA 58.775 45.455 0.00 0.00 0.00 1.90
1607 1951 2.489619 GGCATCCAATCCAGCCTTCATA 60.490 50.000 0.00 0.00 43.70 2.15
1750 2098 7.178983 AGAGAGAGAGACATTCACAAGAAGAAT 59.821 37.037 0.00 0.00 37.14 2.40
1766 2114 6.351881 GGAGACTGACTTTCTAGAGAGAGAGA 60.352 46.154 16.76 0.00 36.26 3.10
1767 2115 5.817816 GGAGACTGACTTTCTAGAGAGAGAG 59.182 48.000 16.76 12.77 39.36 3.20
1821 2173 3.323136 CGCTCGTATCGCCAGCAC 61.323 66.667 0.00 0.00 32.27 4.40
1839 2191 1.678970 GCGCCTTCCCCTTGTCATT 60.679 57.895 0.00 0.00 0.00 2.57
1924 2276 1.402968 CAAGGTGAATCAGAATGGGCG 59.597 52.381 0.00 0.00 36.16 6.13
2017 2369 2.161012 ACGCTCGAACAAGAGAACGATA 59.839 45.455 0.00 0.00 40.57 2.92
2047 2399 1.447838 CCCCACATCCGAAGACGTG 60.448 63.158 0.00 0.00 37.88 4.49
2099 2452 7.770897 ACTTGTAATTAGAGGGCAAATAGTGAG 59.229 37.037 0.00 0.00 0.00 3.51
2133 2486 5.226194 TCAAATGGAAGGGAACAAAATGG 57.774 39.130 0.00 0.00 0.00 3.16
2170 2686 3.455177 TGGTCCTAATAAACCCACGCATA 59.545 43.478 0.00 0.00 34.47 3.14
2175 2691 6.002653 AGAGATTGGTCCTAATAAACCCAC 57.997 41.667 0.00 0.00 34.47 4.61
2320 2836 4.263949 ACAAATAGGAAGGTGGAAAGAGGG 60.264 45.833 0.00 0.00 0.00 4.30
2325 2841 7.235079 TGATACAACAAATAGGAAGGTGGAAA 58.765 34.615 0.00 0.00 0.00 3.13
2337 2853 7.878547 TGAAGGCATCATGATACAACAAATA 57.121 32.000 8.15 0.00 31.50 1.40
2418 2934 5.876357 AGGAGCAAACTTCCAAACTATACA 58.124 37.500 0.00 0.00 0.00 2.29
2607 3123 6.458210 AGTCCAGCAAAAATAAACATCTTGG 58.542 36.000 0.00 0.00 0.00 3.61
2617 3133 3.058293 CAGCACGAAGTCCAGCAAAAATA 60.058 43.478 0.00 0.00 41.61 1.40
2625 3141 2.673368 GGATAAACAGCACGAAGTCCAG 59.327 50.000 0.00 0.00 41.61 3.86
2636 3152 6.017852 GGACTGCATAGTAAAGGATAAACAGC 60.018 42.308 0.00 0.00 37.25 4.40
2672 3188 9.965902 AAAGAACACTCAGTGATTATTTCCTAT 57.034 29.630 13.14 0.00 36.96 2.57
2674 3190 7.721399 ACAAAGAACACTCAGTGATTATTTCCT 59.279 33.333 13.14 0.00 36.96 3.36
2681 3197 7.220030 AGTCATACAAAGAACACTCAGTGATT 58.780 34.615 13.14 1.75 36.96 2.57
2706 3222 9.143155 TGATATGTATTAGCTACCAAGTTCTGA 57.857 33.333 0.00 0.00 0.00 3.27
3160 3677 8.500753 ACAGTATCAACAAGAAGTTTAACACA 57.499 30.769 0.00 0.00 38.74 3.72
3282 3799 1.133976 AGCACCTCTGCATGGGAATAC 60.134 52.381 11.38 0.00 46.97 1.89
4135 4661 9.350357 CTTTTCCACATGAATTTATGTTCTCAG 57.650 33.333 12.81 2.48 39.17 3.35
4184 4710 6.089016 CACTCAAACTGCATCACAAATTCATC 59.911 38.462 0.00 0.00 0.00 2.92
4426 4971 7.382110 CCACCCACATAATTATTCAACACAAA 58.618 34.615 0.00 0.00 0.00 2.83
4439 4984 3.785887 ACAGATACACCCACCCACATAAT 59.214 43.478 0.00 0.00 0.00 1.28
4752 5304 2.945008 TGCAAGATGAATGATCCGAACC 59.055 45.455 0.00 0.00 0.00 3.62
4753 5305 4.142622 TGTTGCAAGATGAATGATCCGAAC 60.143 41.667 0.00 0.00 0.00 3.95
5003 5555 5.538118 CTTATTGTTTTTCAGGACCAACCC 58.462 41.667 0.00 0.00 40.05 4.11
5023 5575 7.120726 TGCATTGCGTACTAGATAGATAGCTTA 59.879 37.037 3.84 0.00 0.00 3.09
5034 5586 6.978343 ACTTAATTTGCATTGCGTACTAGA 57.022 33.333 3.84 0.00 0.00 2.43
5107 5659 4.528504 ACGCCAACAAAACAAAACAAAAC 58.471 34.783 0.00 0.00 0.00 2.43
5108 5660 4.272504 TGACGCCAACAAAACAAAACAAAA 59.727 33.333 0.00 0.00 0.00 2.44
5111 5663 2.731976 GTGACGCCAACAAAACAAAACA 59.268 40.909 0.00 0.00 0.00 2.83
5112 5664 2.990514 AGTGACGCCAACAAAACAAAAC 59.009 40.909 0.00 0.00 0.00 2.43
5113 5665 3.305398 AGTGACGCCAACAAAACAAAA 57.695 38.095 0.00 0.00 0.00 2.44
5254 5806 1.369321 GGAGATCGTCATGGGGCTC 59.631 63.158 0.00 0.00 0.00 4.70
5290 5842 3.753294 ACGAAGAAGAAGAAGAGCCAA 57.247 42.857 0.00 0.00 0.00 4.52
5309 5861 3.137687 CACCAACAAGGGGGCAAC 58.862 61.111 0.00 0.00 43.89 4.17
5353 5905 3.462678 GGCTCCGTGACCTCCTCC 61.463 72.222 0.00 0.00 0.00 4.30
5354 5906 3.827898 CGGCTCCGTGACCTCCTC 61.828 72.222 0.00 0.00 34.35 3.71
5355 5907 4.361971 TCGGCTCCGTGACCTCCT 62.362 66.667 8.28 0.00 40.74 3.69
5365 5917 3.453679 ACGGAGAAGCTCGGCTCC 61.454 66.667 16.34 16.34 45.73 4.70
5494 6046 4.436998 GTCTGCACCCCGAGGTCG 62.437 72.222 0.00 0.00 46.45 4.79


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

AutoCloner maintained by Alex Coulton.