Multiple sequence alignment - TraesCS1A01G236500

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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 TraesCS1A01G236500 chr1A 100.000 4814 0 0 1 4814 418935858 418940671 0.000000e+00 8890.0
1 TraesCS1A01G236500 chr1A 88.548 1109 77 11 3455 4516 421642808 421643913 0.000000e+00 1299.0
2 TraesCS1A01G236500 chr1A 94.993 759 35 3 2307 3064 406598888 406599644 0.000000e+00 1188.0
3 TraesCS1A01G236500 chr1A 95.099 755 35 2 2311 3064 425253839 425253086 0.000000e+00 1188.0
4 TraesCS1A01G236500 chr1A 94.862 759 37 2 2307 3064 421642052 421642809 0.000000e+00 1184.0
5 TraesCS1A01G236500 chr1A 94.992 599 28 1 3455 4053 406599643 406600239 0.000000e+00 939.0
6 TraesCS1A01G236500 chr1A 94.157 599 33 1 3455 4053 407513152 407512556 0.000000e+00 911.0
7 TraesCS1A01G236500 chr1A 93.823 599 35 1 3455 4053 425253087 425252491 0.000000e+00 900.0
8 TraesCS1A01G236500 chr1A 92.178 473 31 4 4048 4516 406600261 406600731 0.000000e+00 664.0
9 TraesCS1A01G236500 chr1A 92.431 436 27 4 4048 4478 425252469 425252035 6.850000e-173 617.0
10 TraesCS1A01G236500 chr1A 92.000 400 26 5 4048 4442 407512534 407512136 1.510000e-154 556.0
11 TraesCS1A01G236500 chr1A 92.581 310 21 2 2756 3064 407513459 407513151 1.230000e-120 444.0
12 TraesCS1A01G236500 chr1A 93.548 124 8 0 4691 4814 419008288 419008411 8.230000e-43 185.0
13 TraesCS1A01G236500 chr1A 96.154 78 2 1 4439 4516 407511816 407511740 5.060000e-25 126.0
14 TraesCS1A01G236500 chr1A 94.595 74 3 1 4517 4589 34176397 34176324 3.940000e-21 113.0
15 TraesCS1A01G236500 chr1D 95.316 3501 114 22 1320 4814 325590249 325586793 0.000000e+00 5511.0
16 TraesCS1A01G236500 chr1D 92.908 1114 47 10 1 1096 325591526 325590427 0.000000e+00 1591.0
17 TraesCS1A01G236500 chr1D 91.339 127 11 0 1097 1223 325590396 325590270 1.780000e-39 174.0
18 TraesCS1A01G236500 chr1B 96.424 1734 51 7 1256 2979 438032868 438031136 0.000000e+00 2848.0
19 TraesCS1A01G236500 chr1B 95.712 1609 47 11 2972 4576 438030928 438029338 0.000000e+00 2569.0
20 TraesCS1A01G236500 chr1B 90.396 833 37 12 1 831 438034456 438033665 0.000000e+00 1055.0
21 TraesCS1A01G236500 chr1B 90.323 155 15 0 1103 1257 438033103 438032949 2.270000e-48 204.0
22 TraesCS1A01G236500 chr1B 99.038 104 1 0 993 1096 438033243 438033140 2.290000e-43 187.0
23 TraesCS1A01G236500 chr1B 96.053 76 2 1 4740 4814 438028858 438028783 6.540000e-24 122.0
24 TraesCS1A01G236500 chrUn 94.215 121 7 0 4694 4814 388760219 388760099 8.230000e-43 185.0
25 TraesCS1A01G236500 chrUn 93.548 124 8 0 4691 4814 390043391 390043514 8.230000e-43 185.0
26 TraesCS1A01G236500 chr2D 94.898 98 5 0 2 99 506282924 506282827 2.320000e-33 154.0
27 TraesCS1A01G236500 chr4D 79.070 215 41 4 4517 4727 73219398 73219184 1.400000e-30 145.0
28 TraesCS1A01G236500 chr3D 92.929 99 7 0 1 99 488892597 488892499 1.400000e-30 145.0
29 TraesCS1A01G236500 chr3D 86.047 86 12 0 4521 4606 184604742 184604657 5.130000e-15 93.5
30 TraesCS1A01G236500 chr5A 85.246 122 17 1 4515 4635 586663221 586663100 1.820000e-24 124.0
31 TraesCS1A01G236500 chr5A 87.912 91 8 3 4518 4606 338221466 338221555 2.370000e-18 104.0
32 TraesCS1A01G236500 chr7A 86.813 91 11 1 4516 4605 459622742 459622832 3.070000e-17 100.0
33 TraesCS1A01G236500 chr2A 76.503 183 31 10 4518 4688 760323921 760323739 6.640000e-14 89.8


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 TraesCS1A01G236500 chr1A 418935858 418940671 4813 False 8890.000000 8890 100.000000 1 4814 1 chr1A.!!$F1 4813
1 TraesCS1A01G236500 chr1A 421642052 421643913 1861 False 1241.500000 1299 91.705000 2307 4516 2 chr1A.!!$F4 2209
2 TraesCS1A01G236500 chr1A 406598888 406600731 1843 False 930.333333 1188 94.054333 2307 4516 3 chr1A.!!$F3 2209
3 TraesCS1A01G236500 chr1A 425252035 425253839 1804 True 901.666667 1188 93.784333 2311 4478 3 chr1A.!!$R3 2167
4 TraesCS1A01G236500 chr1A 407511740 407513459 1719 True 509.250000 911 93.723000 2756 4516 4 chr1A.!!$R2 1760
5 TraesCS1A01G236500 chr1D 325586793 325591526 4733 True 2425.333333 5511 93.187667 1 4814 3 chr1D.!!$R1 4813
6 TraesCS1A01G236500 chr1B 438028783 438034456 5673 True 1164.166667 2848 94.657667 1 4814 6 chr1B.!!$R1 4813

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
570 572 0.030603 ACCTCTCCCCCTCCTCAATC 60.031 60.000 0.0 0.0 0.00 2.67 F
749 751 0.479378 TACCGCCCCCTTCAACTTTT 59.521 50.000 0.0 0.0 0.00 2.27 F
966 1214 2.187599 CTGAAGGGCGGTTTTGCTCG 62.188 60.000 0.0 0.0 41.40 5.03 F
1143 1436 2.351276 CCCTGCTTGCCGGTTAGT 59.649 61.111 1.9 0.0 0.00 2.24 F
2338 2724 2.629137 TGAAAATGCTGGTTCATGCACT 59.371 40.909 0.0 0.0 42.26 4.40 F
3253 3855 2.225369 ACCCCCGTACTACCAGTACTTT 60.225 50.000 13.1 0.0 46.68 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1431 1812 2.946329 TGGCGCTTGTCTTTTGTTCTTA 59.054 40.909 7.64 0.0 0.00 2.10 R
2313 2699 3.615496 GCATGAACCAGCATTTTCATCAC 59.385 43.478 0.00 0.0 39.86 3.06 R
2882 3268 5.686159 AGAAGAACAAGCACAGAAATCAG 57.314 39.130 0.00 0.0 0.00 2.90 R
3043 3645 4.263905 ACCATGGTGGCTAAAATCAGAAGA 60.264 41.667 18.99 0.0 42.67 2.87 R
3615 4217 0.895530 TTCCACTCACGGACCTGATC 59.104 55.000 0.00 0.0 33.75 2.92 R
4689 6080 0.176910 TGTGACACGAAGCACTCCAA 59.823 50.000 0.22 0.0 36.05 3.53 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
228 229 3.053455 GAGCGAGCCACATACATACTTC 58.947 50.000 0.00 0.00 0.00 3.01
259 260 1.402968 GCGTATACAGAGGAACGGTGA 59.597 52.381 3.32 0.00 35.93 4.02
312 313 1.792118 CGATGGCTATGTCGTCGGGA 61.792 60.000 5.96 0.00 42.06 5.14
406 407 2.610433 CGATTCTGCAGTGTCAAGCTA 58.390 47.619 14.67 0.00 0.00 3.32
526 527 2.738938 GCGTACCCCGGGGATTCTT 61.739 63.158 46.68 26.04 38.96 2.52
538 539 1.025041 GGATTCTTTGTGGCGGATCC 58.975 55.000 0.00 0.00 0.00 3.36
570 572 0.030603 ACCTCTCCCCCTCCTCAATC 60.031 60.000 0.00 0.00 0.00 2.67
651 653 6.945218 TCAAATTAAAACGCCCCTAGTAGTA 58.055 36.000 0.00 0.00 0.00 1.82
652 654 7.043565 TCAAATTAAAACGCCCCTAGTAGTAG 58.956 38.462 0.00 0.00 0.00 2.57
653 655 6.550938 AATTAAAACGCCCCTAGTAGTAGT 57.449 37.500 3.91 0.00 0.00 2.73
654 656 7.660030 AATTAAAACGCCCCTAGTAGTAGTA 57.340 36.000 3.91 0.00 0.00 1.82
710 712 5.278660 GGAGACCGCGGATTATTTTACTCTA 60.279 44.000 35.90 0.00 0.00 2.43
711 713 5.527033 AGACCGCGGATTATTTTACTCTAC 58.473 41.667 35.90 0.00 0.00 2.59
712 714 5.301298 AGACCGCGGATTATTTTACTCTACT 59.699 40.000 35.90 1.36 0.00 2.57
713 715 5.527033 ACCGCGGATTATTTTACTCTACTC 58.473 41.667 35.90 0.00 0.00 2.59
714 716 4.922103 CCGCGGATTATTTTACTCTACTCC 59.078 45.833 24.07 0.00 0.00 3.85
715 717 4.615961 CGCGGATTATTTTACTCTACTCCG 59.384 45.833 0.00 3.43 40.89 4.63
716 718 5.527033 GCGGATTATTTTACTCTACTCCGT 58.473 41.667 9.13 0.00 40.39 4.69
749 751 0.479378 TACCGCCCCCTTCAACTTTT 59.521 50.000 0.00 0.00 0.00 2.27
775 777 8.821147 TGCCATATATACGTATTTTCTTTCGT 57.179 30.769 14.33 0.00 39.74 3.85
885 888 2.586357 GATTGCCCCTCGCTCGAC 60.586 66.667 0.00 0.00 38.78 4.20
943 946 3.918220 CGCGCGCAGACAGAATCC 61.918 66.667 32.61 0.00 0.00 3.01
966 1214 2.187599 CTGAAGGGCGGTTTTGCTCG 62.188 60.000 0.00 0.00 41.40 5.03
1143 1436 2.351276 CCCTGCTTGCCGGTTAGT 59.649 61.111 1.90 0.00 0.00 2.24
1181 1474 3.119029 GGCAATGTTGTGGCTATGTTCAT 60.119 43.478 0.00 0.00 40.77 2.57
1184 1477 5.337554 CAATGTTGTGGCTATGTTCATGAG 58.662 41.667 0.00 0.00 0.00 2.90
1195 1488 5.861251 GCTATGTTCATGAGTCGATTAGGAG 59.139 44.000 0.00 0.00 0.00 3.69
1199 1492 5.216648 GTTCATGAGTCGATTAGGAGCTAC 58.783 45.833 0.00 0.00 0.00 3.58
1211 1504 3.560636 AGGAGCTACAACGCCATTATT 57.439 42.857 0.00 0.00 30.84 1.40
1219 1512 3.085533 ACAACGCCATTATTAACCAGCA 58.914 40.909 0.00 0.00 0.00 4.41
1225 1518 4.672409 GCCATTATTAACCAGCAGTTGTC 58.328 43.478 2.63 0.00 39.67 3.18
1253 1546 5.065859 TCACTAGTTCACCACATGTTGTTTG 59.934 40.000 0.00 0.00 0.00 2.93
1270 1645 7.648142 TGTTGTTTGATACTTTGATTGACTCC 58.352 34.615 0.00 0.00 0.00 3.85
1285 1660 3.664107 TGACTCCTGTTATGTGCTCAAC 58.336 45.455 0.00 0.00 0.00 3.18
1286 1661 3.324846 TGACTCCTGTTATGTGCTCAACT 59.675 43.478 0.00 0.00 0.00 3.16
1287 1662 3.929610 GACTCCTGTTATGTGCTCAACTC 59.070 47.826 0.00 0.00 0.00 3.01
1431 1812 6.039829 GGTCCTGTTTTCTTCATTCAGAACTT 59.960 38.462 0.00 0.00 32.28 2.66
1506 1887 5.419155 TGCAGAGTATACTTCAGCAGTAAGT 59.581 40.000 18.18 4.16 41.56 2.24
1526 1907 3.817647 AGTTTGCCTGTCATCTTGTCTTC 59.182 43.478 0.00 0.00 0.00 2.87
1589 1970 7.033185 CCAGTAGTAATGGGTTTAAACATTGC 58.967 38.462 19.57 14.05 39.14 3.56
2159 2545 8.206325 TGAAGTCTTGCTCAATCAGATAAATC 57.794 34.615 0.00 0.00 0.00 2.17
2309 2695 2.887151 AGGTCAGCATGGCTAAAGTT 57.113 45.000 0.00 0.00 43.10 2.66
2313 2699 3.989817 GGTCAGCATGGCTAAAGTTTTTG 59.010 43.478 0.00 0.00 43.10 2.44
2338 2724 2.629137 TGAAAATGCTGGTTCATGCACT 59.371 40.909 0.00 0.00 42.26 4.40
2528 2914 3.410631 TCGTTTTGTGCCCTTGATCTA 57.589 42.857 0.00 0.00 0.00 1.98
2535 2921 3.355378 TGTGCCCTTGATCTAATTGTGG 58.645 45.455 0.00 0.00 0.00 4.17
2699 3085 8.202461 TCCTCCTCTGTTCTTAGTTTTAATCA 57.798 34.615 0.00 0.00 0.00 2.57
2805 3191 8.370940 TCAGACTGAACTCTCTTTACATTTGAT 58.629 33.333 1.64 0.00 0.00 2.57
2986 3587 9.216117 GTACACCTTCTGTATATTTGAACAGTT 57.784 33.333 3.82 0.00 42.96 3.16
3043 3645 8.463930 TTTGTCATCCTGAAAAGTAAGACATT 57.536 30.769 0.00 0.00 35.06 2.71
3253 3855 2.225369 ACCCCCGTACTACCAGTACTTT 60.225 50.000 13.10 0.00 46.68 2.66
3291 3893 4.283467 CCATCATTTCCCACGAGAGGTATA 59.717 45.833 0.00 0.00 0.00 1.47
3303 3905 4.272991 ACGAGAGGTATACATCGTTCTGTC 59.727 45.833 18.60 7.77 45.39 3.51
3443 4045 7.359595 GCGCATTTCACATATATTTTCAGGTA 58.640 34.615 0.30 0.00 0.00 3.08
3615 4217 5.452078 TTCACCCTAACATTGCTTTTCTG 57.548 39.130 0.00 0.00 0.00 3.02
3616 4218 4.724399 TCACCCTAACATTGCTTTTCTGA 58.276 39.130 0.00 0.00 0.00 3.27
3669 4271 5.311649 AGACCATATCCACTATCTTGGCATT 59.688 40.000 0.00 0.00 36.48 3.56
3893 4496 2.420628 TCTTGTTGGCAATCAAAGCG 57.579 45.000 1.92 0.00 37.08 4.68
3965 4568 4.213564 AGCTGAGGGTGTATTTCTGAAG 57.786 45.455 0.00 0.00 0.00 3.02
4113 4773 7.492020 TGTTTTCAAAAATGTTGAGGATGTCTG 59.508 33.333 0.00 0.00 0.00 3.51
4234 4896 9.383519 TGTGGTAAAAATTTAAAAATCTGCACA 57.616 25.926 0.00 0.00 0.00 4.57
4252 4914 9.698309 ATCTGCACAACTATAGTACATACATTC 57.302 33.333 5.65 0.00 0.00 2.67
4336 5002 1.564348 ACAGACTGAACACAAGGGGTT 59.436 47.619 10.08 0.00 0.00 4.11
4531 5535 5.896073 AATAGAAGGACCCTGATAAGTGG 57.104 43.478 0.00 0.00 0.00 4.00
4567 5571 2.910688 ACACATGACAACTCCGAACT 57.089 45.000 0.00 0.00 0.00 3.01
4599 5603 8.642908 TGACAAGTTTAGTAATACGATGATGG 57.357 34.615 0.00 0.00 0.00 3.51
4606 5610 7.709269 TTAGTAATACGATGATGGCAACTTC 57.291 36.000 0.00 0.00 41.00 3.01
4612 5616 3.573967 ACGATGATGGCAACTTCCTTTTT 59.426 39.130 0.00 0.00 39.92 1.94
4615 5619 2.368221 TGATGGCAACTTCCTTTTTGGG 59.632 45.455 0.00 0.00 39.92 4.12
4701 6092 1.270625 TGTTAGGGTTGGAGTGCTTCG 60.271 52.381 0.00 0.00 0.00 3.79
4704 6095 1.227853 GGGTTGGAGTGCTTCGTGT 60.228 57.895 0.00 0.00 0.00 4.49
4709 6100 0.249447 TGGAGTGCTTCGTGTCACAG 60.249 55.000 3.42 0.00 35.76 3.66
4714 6105 0.747852 TGCTTCGTGTCACAGGTGTA 59.252 50.000 3.42 0.00 0.00 2.90
4715 6106 1.137282 TGCTTCGTGTCACAGGTGTAA 59.863 47.619 3.42 0.00 0.00 2.41
4716 6107 1.525619 GCTTCGTGTCACAGGTGTAAC 59.474 52.381 3.42 0.00 0.00 2.50
4722 6113 3.488310 CGTGTCACAGGTGTAACACTTAC 59.512 47.826 13.44 0.00 39.98 2.34
4797 6188 2.646930 TGTTGGAGCATATGGAAGCAG 58.353 47.619 4.56 0.00 0.00 4.24
4811 6202 9.330063 CATATGGAAGCAGAGAAATAGTACAAA 57.670 33.333 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
241 242 4.197750 TCTCTCACCGTTCCTCTGTATAC 58.802 47.826 0.00 0.00 0.00 1.47
259 260 3.073735 CCAGGTGCGCCTCTCTCT 61.074 66.667 18.11 0.00 44.97 3.10
406 407 1.595794 CCGACACAAAGCAGTTACGTT 59.404 47.619 0.00 0.00 0.00 3.99
517 518 0.395724 ATCCGCCACAAAGAATCCCC 60.396 55.000 0.00 0.00 0.00 4.81
526 527 2.577059 GAGACGGATCCGCCACAA 59.423 61.111 33.62 0.00 44.19 3.33
538 539 4.477975 GAGGTGCGACCCGAGACG 62.478 72.222 2.18 0.00 39.75 4.18
570 572 3.192922 GGTCGCCGTCGGGAATTG 61.193 66.667 14.38 0.00 36.13 2.32
617 619 5.288472 GGCGTTTTAATTTGATTAGGTGCTG 59.712 40.000 0.00 0.00 0.00 4.41
711 713 7.804600 GGGCGGTAAATAAAATAAAATACGGAG 59.195 37.037 0.00 0.00 0.00 4.63
712 714 7.255416 GGGGCGGTAAATAAAATAAAATACGGA 60.255 37.037 0.00 0.00 0.00 4.69
713 715 6.862608 GGGGCGGTAAATAAAATAAAATACGG 59.137 38.462 0.00 0.00 0.00 4.02
714 716 6.862608 GGGGGCGGTAAATAAAATAAAATACG 59.137 38.462 0.00 0.00 0.00 3.06
715 717 7.954835 AGGGGGCGGTAAATAAAATAAAATAC 58.045 34.615 0.00 0.00 0.00 1.89
716 718 8.550280 AAGGGGGCGGTAAATAAAATAAAATA 57.450 30.769 0.00 0.00 0.00 1.40
749 751 9.263538 ACGAAAGAAAATACGTATATATGGCAA 57.736 29.630 8.83 0.00 37.22 4.52
775 777 1.072332 TGCAGGGCAAGCGAAAGTA 59.928 52.632 0.00 0.00 34.76 2.24
777 779 1.799258 AAGTGCAGGGCAAGCGAAAG 61.799 55.000 0.00 0.00 41.47 2.62
841 844 1.958359 ATTAGGGAGGGGAGGGGGT 60.958 63.158 0.00 0.00 0.00 4.95
848 851 4.729552 TCAATCAATGATTAGGGAGGGG 57.270 45.455 8.29 0.00 31.50 4.79
885 888 4.468689 GGAGAAACCTCGGCCCGG 62.469 72.222 1.90 0.00 35.41 5.73
929 932 2.125512 ACCGGATTCTGTCTGCGC 60.126 61.111 9.46 0.00 31.43 6.09
943 946 1.599797 AAAACCGCCCTTCAGACCG 60.600 57.895 0.00 0.00 0.00 4.79
950 1198 2.983592 CCGAGCAAAACCGCCCTT 60.984 61.111 0.00 0.00 0.00 3.95
1131 1424 0.321653 AGGCAAGACTAACCGGCAAG 60.322 55.000 0.00 0.63 0.00 4.01
1143 1436 3.003173 CCCTGACCCGAGGCAAGA 61.003 66.667 0.00 0.00 0.00 3.02
1181 1474 3.064958 CGTTGTAGCTCCTAATCGACTCA 59.935 47.826 0.00 0.00 0.00 3.41
1184 1477 2.117910 GCGTTGTAGCTCCTAATCGAC 58.882 52.381 0.00 0.00 0.00 4.20
1195 1488 4.788521 GCTGGTTAATAATGGCGTTGTAGC 60.789 45.833 1.27 0.00 0.00 3.58
1199 1492 3.128589 ACTGCTGGTTAATAATGGCGTTG 59.871 43.478 1.27 0.00 0.00 4.10
1219 1512 3.069729 GGTGAACTAGTGACCAGACAACT 59.930 47.826 16.25 0.00 0.00 3.16
1225 1518 3.244215 ACATGTGGTGAACTAGTGACCAG 60.244 47.826 21.92 15.03 40.46 4.00
1228 1521 4.127171 ACAACATGTGGTGAACTAGTGAC 58.873 43.478 4.67 0.00 35.97 3.67
1233 1526 6.995686 AGTATCAAACAACATGTGGTGAACTA 59.004 34.615 6.65 0.00 35.97 2.24
1253 1546 8.607459 CACATAACAGGAGTCAATCAAAGTATC 58.393 37.037 0.00 0.00 0.00 2.24
1270 1645 5.437289 TTTTGGAGTTGAGCACATAACAG 57.563 39.130 0.00 0.00 0.00 3.16
1304 1681 1.133823 AGGATGACAAGGTGTGCACAA 60.134 47.619 23.59 3.99 0.00 3.33
1308 1685 1.446907 CAGAGGATGACAAGGTGTGC 58.553 55.000 0.00 0.00 0.00 4.57
1311 1688 2.189594 TTGCAGAGGATGACAAGGTG 57.810 50.000 0.00 0.00 0.00 4.00
1364 1745 3.796717 GCGTTGAGTAATCGATCATGACA 59.203 43.478 0.00 0.00 0.00 3.58
1431 1812 2.946329 TGGCGCTTGTCTTTTGTTCTTA 59.054 40.909 7.64 0.00 0.00 2.10
1506 1887 4.090761 AGAAGACAAGATGACAGGCAAA 57.909 40.909 0.00 0.00 0.00 3.68
1526 1907 6.674694 AGAAATCTGAATTGGACGATGAAG 57.325 37.500 0.00 0.00 0.00 3.02
1560 1941 9.847224 ATGTTTAAACCCATTACTACTGGATAG 57.153 33.333 15.59 0.00 35.70 2.08
2159 2545 4.134379 AGCAGGATGTGAACTATGTCAG 57.866 45.455 0.00 0.00 39.31 3.51
2309 2695 5.668471 TGAACCAGCATTTTCATCACAAAA 58.332 33.333 0.00 0.00 0.00 2.44
2313 2699 3.615496 GCATGAACCAGCATTTTCATCAC 59.385 43.478 0.00 0.00 39.86 3.06
2528 2914 6.663093 TCAGACAAATATTAGCACCCACAATT 59.337 34.615 0.00 0.00 0.00 2.32
2535 2921 7.849804 TCTTCTTCAGACAAATATTAGCACC 57.150 36.000 0.00 0.00 0.00 5.01
2585 2971 8.501070 AGGAGGATGAATTCATGAAAAGTAGAT 58.499 33.333 25.37 0.00 36.57 1.98
2882 3268 5.686159 AGAAGAACAAGCACAGAAATCAG 57.314 39.130 0.00 0.00 0.00 2.90
2925 3311 6.472016 TGAACAAAGATAGTTACATCTGCCA 58.528 36.000 0.00 0.00 35.42 4.92
3003 3604 5.581085 GGATGACAAAAACAGACGCTAGTAT 59.419 40.000 0.00 0.00 0.00 2.12
3043 3645 4.263905 ACCATGGTGGCTAAAATCAGAAGA 60.264 41.667 18.99 0.00 42.67 2.87
3253 3855 4.927267 ATGATGGTAGGTTTTCTGTGGA 57.073 40.909 0.00 0.00 0.00 4.02
3291 3893 2.628178 TGGAAGTGAGACAGAACGATGT 59.372 45.455 0.00 0.00 35.68 3.06
3303 3905 5.940470 AGTTATTAGCAAAGGTGGAAGTGAG 59.060 40.000 0.00 0.00 0.00 3.51
3338 3940 7.448469 AGAAAAGCATAAACATCAGGTGTAAGT 59.552 33.333 0.00 0.00 41.14 2.24
3339 3941 7.752239 CAGAAAAGCATAAACATCAGGTGTAAG 59.248 37.037 0.00 0.00 41.14 2.34
3340 3942 7.309133 CCAGAAAAGCATAAACATCAGGTGTAA 60.309 37.037 0.00 0.00 41.14 2.41
3341 3943 6.150976 CCAGAAAAGCATAAACATCAGGTGTA 59.849 38.462 0.00 0.00 41.14 2.90
3342 3944 5.047802 CCAGAAAAGCATAAACATCAGGTGT 60.048 40.000 0.00 0.00 44.84 4.16
3343 3945 5.404946 CCAGAAAAGCATAAACATCAGGTG 58.595 41.667 0.00 0.00 0.00 4.00
3344 3946 4.463891 CCCAGAAAAGCATAAACATCAGGT 59.536 41.667 0.00 0.00 0.00 4.00
3345 3947 4.706476 TCCCAGAAAAGCATAAACATCAGG 59.294 41.667 0.00 0.00 0.00 3.86
3346 3948 5.649395 TCTCCCAGAAAAGCATAAACATCAG 59.351 40.000 0.00 0.00 0.00 2.90
3443 4045 6.433847 TCGAGTCCAATATTATGAACCCAT 57.566 37.500 0.00 0.00 36.81 4.00
3615 4217 0.895530 TTCCACTCACGGACCTGATC 59.104 55.000 0.00 0.00 33.75 2.92
3616 4218 1.348064 TTTCCACTCACGGACCTGAT 58.652 50.000 0.00 0.00 33.75 2.90
3669 4271 1.528161 CGCGAATCAGAATGCATGCTA 59.472 47.619 20.33 5.73 34.76 3.49
3681 4283 2.597713 GCATGATCCGCGCGAATCA 61.598 57.895 33.26 33.26 0.00 2.57
3684 4286 3.264159 CTGCATGATCCGCGCGAA 61.264 61.111 34.63 13.54 0.00 4.70
3857 4460 7.870445 GCCAACAAGAATATTGTACTTTGGAAA 59.130 33.333 17.41 0.00 31.55 3.13
3858 4461 7.014711 TGCCAACAAGAATATTGTACTTTGGAA 59.985 33.333 17.41 9.02 31.55 3.53
3859 4462 6.491745 TGCCAACAAGAATATTGTACTTTGGA 59.508 34.615 17.41 6.18 31.55 3.53
3893 4496 5.505100 CGCGCGTATATATACATGAGATAGC 59.495 44.000 24.19 12.38 32.87 2.97
4035 4638 5.948758 TCACCATACATAATGAAAGCAACCA 59.051 36.000 0.00 0.00 37.86 3.67
4113 4773 6.512297 AGGAATGTCAAAAACCATTGTGTAC 58.488 36.000 0.00 0.00 31.67 2.90
4252 4914 4.279169 ACGCTTGATTTCCATATCCAATGG 59.721 41.667 0.00 0.00 40.48 3.16
4362 5028 9.897744 ACACATAAACACATCTGTTATTTTCTG 57.102 29.630 0.00 0.00 39.88 3.02
4363 5029 9.897744 CACACATAAACACATCTGTTATTTTCT 57.102 29.630 0.00 0.00 39.88 2.52
4531 5535 1.370414 GTTCGTGCCACATGTGTGC 60.370 57.895 23.79 23.98 44.34 4.57
4577 5581 7.477144 TGCCATCATCGTATTACTAAACTTG 57.523 36.000 0.00 0.00 0.00 3.16
4578 5582 7.769044 AGTTGCCATCATCGTATTACTAAACTT 59.231 33.333 0.00 0.00 0.00 2.66
4579 5583 7.272978 AGTTGCCATCATCGTATTACTAAACT 58.727 34.615 0.00 0.00 0.00 2.66
4580 5584 7.478520 AGTTGCCATCATCGTATTACTAAAC 57.521 36.000 0.00 0.00 0.00 2.01
4581 5585 7.225931 GGAAGTTGCCATCATCGTATTACTAAA 59.774 37.037 0.00 0.00 0.00 1.85
4582 5586 6.704493 GGAAGTTGCCATCATCGTATTACTAA 59.296 38.462 0.00 0.00 0.00 2.24
4583 5587 6.041637 AGGAAGTTGCCATCATCGTATTACTA 59.958 38.462 0.00 0.00 0.00 1.82
4584 5588 5.057149 GGAAGTTGCCATCATCGTATTACT 58.943 41.667 0.00 0.00 0.00 2.24
4585 5589 5.057149 AGGAAGTTGCCATCATCGTATTAC 58.943 41.667 0.00 0.00 0.00 1.89
4586 5590 5.290493 AGGAAGTTGCCATCATCGTATTA 57.710 39.130 0.00 0.00 0.00 0.98
4587 5591 4.156455 AGGAAGTTGCCATCATCGTATT 57.844 40.909 0.00 0.00 0.00 1.89
4588 5592 3.845781 AGGAAGTTGCCATCATCGTAT 57.154 42.857 0.00 0.00 0.00 3.06
4589 5593 3.627395 AAGGAAGTTGCCATCATCGTA 57.373 42.857 0.00 0.00 0.00 3.43
4590 5594 2.496899 AAGGAAGTTGCCATCATCGT 57.503 45.000 0.00 0.00 0.00 3.73
4591 5595 3.855689 AAAAGGAAGTTGCCATCATCG 57.144 42.857 0.00 0.00 0.00 3.84
4592 5596 4.248058 CCAAAAAGGAAGTTGCCATCATC 58.752 43.478 0.00 0.00 41.22 2.92
4593 5597 3.008266 CCCAAAAAGGAAGTTGCCATCAT 59.992 43.478 0.00 0.00 41.22 2.45
4594 5598 2.368221 CCCAAAAAGGAAGTTGCCATCA 59.632 45.455 0.00 0.00 41.22 3.07
4595 5599 2.368548 ACCCAAAAAGGAAGTTGCCATC 59.631 45.455 0.00 0.00 41.22 3.51
4596 5600 2.104622 CACCCAAAAAGGAAGTTGCCAT 59.895 45.455 0.00 0.00 41.22 4.40
4597 5601 1.484240 CACCCAAAAAGGAAGTTGCCA 59.516 47.619 0.00 0.00 41.22 4.92
4598 5602 1.202639 CCACCCAAAAAGGAAGTTGCC 60.203 52.381 0.00 0.00 41.22 4.52
4599 5603 1.810031 GCCACCCAAAAAGGAAGTTGC 60.810 52.381 0.00 0.00 41.22 4.17
4606 5610 3.549794 TGAAAATTGCCACCCAAAAAGG 58.450 40.909 0.00 0.00 36.92 3.11
4612 5616 3.922171 AAAACTGAAAATTGCCACCCA 57.078 38.095 0.00 0.00 0.00 4.51
4681 6072 1.270625 CGAAGCACTCCAACCCTAACA 60.271 52.381 0.00 0.00 0.00 2.41
4684 6075 0.320374 CACGAAGCACTCCAACCCTA 59.680 55.000 0.00 0.00 0.00 3.53
4688 6079 0.582005 GTGACACGAAGCACTCCAAC 59.418 55.000 0.00 0.00 32.44 3.77
4689 6080 0.176910 TGTGACACGAAGCACTCCAA 59.823 50.000 0.22 0.00 36.05 3.53
4692 6083 0.249489 ACCTGTGACACGAAGCACTC 60.249 55.000 0.22 0.00 36.05 3.51
4704 6095 4.967084 ATGGTAAGTGTTACACCTGTGA 57.033 40.909 12.28 0.00 37.88 3.58
4709 6100 7.748691 TTTCCTAAATGGTAAGTGTTACACC 57.251 36.000 12.28 0.00 37.88 4.16
4715 6106 8.903820 GCATTCTATTTCCTAAATGGTAAGTGT 58.096 33.333 0.00 0.00 37.07 3.55
4716 6107 8.352942 GGCATTCTATTTCCTAAATGGTAAGTG 58.647 37.037 0.00 0.00 37.07 3.16
4722 6113 7.874528 GGAATTGGCATTCTATTTCCTAAATGG 59.125 37.037 0.00 0.00 39.17 3.16


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

AutoCloner maintained by Alex Coulton.