Multiple sequence alignment - TraesCS7A01G209500

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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 TraesCS7A01G209500 chr7A 100.000 3359 0 0 1 3359 172236057 172232699 0.000000e+00 6204.0
1 TraesCS7A01G209500 chr7A 92.515 1149 73 9 2124 3265 171946779 171945637 0.000000e+00 1633.0
2 TraesCS7A01G209500 chr7A 92.110 1090 59 12 598 1663 171536723 171535637 0.000000e+00 1511.0
3 TraesCS7A01G209500 chr7A 92.110 1090 59 12 598 1663 171950341 171949255 0.000000e+00 1511.0
4 TraesCS7A01G209500 chr7A 91.435 934 69 6 739 1663 171877111 171876180 0.000000e+00 1271.0
5 TraesCS7A01G209500 chr7A 90.000 330 12 1 1757 2086 171438601 171438293 1.120000e-109 407.0
6 TraesCS7A01G209500 chr7A 88.732 71 8 0 12 82 547971552 547971622 1.660000e-13 87.9
7 TraesCS7A01G209500 chr7B 87.419 2456 143 32 581 2961 135036834 135034470 0.000000e+00 2671.0
8 TraesCS7A01G209500 chr7B 90.161 1118 73 16 2141 3227 135018252 135017141 0.000000e+00 1421.0
9 TraesCS7A01G209500 chr7B 91.632 956 73 7 713 1663 134492068 134493021 0.000000e+00 1315.0
10 TraesCS7A01G209500 chr7B 86.876 1082 83 25 1730 2788 128437519 128438564 0.000000e+00 1157.0
11 TraesCS7A01G209500 chr7B 86.180 890 69 18 1730 2612 128070206 128069364 0.000000e+00 913.0
12 TraesCS7A01G209500 chr7B 87.215 657 50 14 2485 3124 134635083 134634444 0.000000e+00 717.0
13 TraesCS7A01G209500 chr7B 78.746 574 103 13 1 565 658193005 658192442 1.900000e-97 366.0
14 TraesCS7A01G209500 chr7D 93.292 1610 77 16 1764 3359 169440121 169438529 0.000000e+00 2346.0
15 TraesCS7A01G209500 chr7D 89.164 1615 105 33 1762 3359 169025360 169026921 0.000000e+00 1949.0
16 TraesCS7A01G209500 chr7D 92.086 1213 70 17 2127 3319 169497935 169496729 0.000000e+00 1685.0
17 TraesCS7A01G209500 chr7D 93.380 1133 64 6 566 1690 168990533 168991662 0.000000e+00 1666.0
18 TraesCS7A01G209500 chr7D 91.622 1110 77 8 597 1690 169422988 169421879 0.000000e+00 1520.0
19 TraesCS7A01G209500 chr7D 90.576 1093 84 10 786 1860 169499206 169498115 0.000000e+00 1430.0
20 TraesCS7A01G209500 chr7D 89.775 1066 63 19 634 1663 169540918 169539863 0.000000e+00 1323.0
21 TraesCS7A01G209500 chr7D 94.903 824 41 1 910 1732 169441030 169440207 0.000000e+00 1288.0
22 TraesCS7A01G209500 chr7D 89.672 1036 56 11 1762 2788 169421732 169420739 0.000000e+00 1273.0
23 TraesCS7A01G209500 chr7D 87.228 1057 85 18 1730 2772 165118979 165119999 0.000000e+00 1158.0
24 TraesCS7A01G209500 chr7D 86.385 1065 80 21 1730 2773 164751904 164750884 0.000000e+00 1103.0
25 TraesCS7A01G209500 chr7D 84.250 400 24 9 1687 2086 168991710 168992070 1.480000e-93 353.0
26 TraesCS7A01G209500 chr7D 77.897 561 97 17 18 565 184212085 184212631 1.160000e-84 324.0
27 TraesCS7A01G209500 chr7D 90.411 73 7 0 1687 1759 169025261 169025333 2.760000e-16 97.1
28 TraesCS7A01G209500 chr6A 87.862 1656 98 37 1687 3319 124423775 124425350 0.000000e+00 1849.0
29 TraesCS7A01G209500 chr6A 91.503 918 63 7 786 1690 124422812 124423727 0.000000e+00 1249.0
30 TraesCS7A01G209500 chr6A 91.285 918 65 10 786 1690 124917059 124916144 0.000000e+00 1238.0
31 TraesCS7A01G209500 chr6A 79.860 571 100 9 1 565 602963659 602964220 1.450000e-108 403.0
32 TraesCS7A01G209500 chrUn 92.515 1149 73 9 2124 3265 262506670 262507812 0.000000e+00 1633.0
33 TraesCS7A01G209500 chrUn 92.515 1149 73 9 2124 3265 326639255 326640397 0.000000e+00 1633.0
34 TraesCS7A01G209500 chrUn 92.110 1090 59 12 598 1663 262505029 262506115 0.000000e+00 1511.0
35 TraesCS7A01G209500 chrUn 91.322 991 50 15 1808 2788 218480268 218481232 0.000000e+00 1321.0
36 TraesCS7A01G209500 chrUn 91.542 934 68 6 739 1663 342997736 342996805 0.000000e+00 1277.0
37 TraesCS7A01G209500 chrUn 88.889 1026 75 13 681 1690 244606725 244607727 0.000000e+00 1227.0
38 TraesCS7A01G209500 chrUn 82.574 373 23 10 1687 2059 262506329 262506659 1.180000e-74 291.0
39 TraesCS7A01G209500 chrUn 82.574 373 23 10 1687 2059 326638914 326639244 1.180000e-74 291.0
40 TraesCS7A01G209500 chrUn 100.000 71 0 0 3289 3359 408774626 408774556 7.560000e-27 132.0
41 TraesCS7A01G209500 chr6D 89.119 1112 64 21 1687 2788 103083910 103084974 0.000000e+00 1330.0
42 TraesCS7A01G209500 chr6D 88.694 1026 77 13 681 1690 103051553 103052555 0.000000e+00 1216.0
43 TraesCS7A01G209500 chr6D 83.111 225 38 0 12 236 373414475 373414699 4.390000e-49 206.0
44 TraesCS7A01G209500 chr4D 90.877 570 41 8 2747 3312 484948444 484947882 0.000000e+00 754.0
45 TraesCS7A01G209500 chr4D 90.543 571 44 7 2747 3313 249283392 249283956 0.000000e+00 747.0
46 TraesCS7A01G209500 chr4D 81.935 310 54 1 12 321 12185111 12185418 9.240000e-66 261.0
47 TraesCS7A01G209500 chr3A 93.855 358 9 3 120 471 699606664 699606314 8.250000e-146 527.0
48 TraesCS7A01G209500 chr3A 76.710 541 102 17 15 542 747742634 747742105 2.550000e-71 279.0
49 TraesCS7A01G209500 chr3A 96.377 138 5 0 1 138 699606912 699606775 9.380000e-56 228.0
50 TraesCS7A01G209500 chr1A 80.070 572 97 12 1 565 551730938 551731499 3.120000e-110 409.0
51 TraesCS7A01G209500 chr1B 81.452 496 78 7 18 507 649657336 649656849 8.740000e-106 394.0
52 TraesCS7A01G209500 chr1B 80.868 507 84 5 18 518 52152448 52151949 1.460000e-103 387.0
53 TraesCS7A01G209500 chr5B 79.304 575 101 10 1 565 582903438 582904004 1.460000e-103 387.0
54 TraesCS7A01G209500 chr2B 80.868 507 84 4 18 518 793983591 793983092 1.460000e-103 387.0
55 TraesCS7A01G209500 chr6B 77.972 572 110 10 1 565 129491842 129492404 8.920000e-91 344.0
56 TraesCS7A01G209500 chr3B 78.237 556 106 6 17 565 787401498 787400951 3.210000e-90 342.0
57 TraesCS7A01G209500 chr2A 78.075 561 96 17 18 565 773298991 773298445 2.500000e-86 329.0


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 TraesCS7A01G209500 chr7A 172232699 172236057 3358 True 6204.00 6204 100.000000 1 3359 1 chr7A.!!$R4 3358
1 TraesCS7A01G209500 chr7A 171945637 171950341 4704 True 1572.00 1633 92.312500 598 3265 2 chr7A.!!$R5 2667
2 TraesCS7A01G209500 chr7A 171535637 171536723 1086 True 1511.00 1511 92.110000 598 1663 1 chr7A.!!$R2 1065
3 TraesCS7A01G209500 chr7A 171876180 171877111 931 True 1271.00 1271 91.435000 739 1663 1 chr7A.!!$R3 924
4 TraesCS7A01G209500 chr7B 135034470 135036834 2364 True 2671.00 2671 87.419000 581 2961 1 chr7B.!!$R4 2380
5 TraesCS7A01G209500 chr7B 135017141 135018252 1111 True 1421.00 1421 90.161000 2141 3227 1 chr7B.!!$R3 1086
6 TraesCS7A01G209500 chr7B 134492068 134493021 953 False 1315.00 1315 91.632000 713 1663 1 chr7B.!!$F2 950
7 TraesCS7A01G209500 chr7B 128437519 128438564 1045 False 1157.00 1157 86.876000 1730 2788 1 chr7B.!!$F1 1058
8 TraesCS7A01G209500 chr7B 128069364 128070206 842 True 913.00 913 86.180000 1730 2612 1 chr7B.!!$R1 882
9 TraesCS7A01G209500 chr7B 134634444 134635083 639 True 717.00 717 87.215000 2485 3124 1 chr7B.!!$R2 639
10 TraesCS7A01G209500 chr7B 658192442 658193005 563 True 366.00 366 78.746000 1 565 1 chr7B.!!$R5 564
11 TraesCS7A01G209500 chr7D 169438529 169441030 2501 True 1817.00 2346 94.097500 910 3359 2 chr7D.!!$R4 2449
12 TraesCS7A01G209500 chr7D 169496729 169499206 2477 True 1557.50 1685 91.331000 786 3319 2 chr7D.!!$R5 2533
13 TraesCS7A01G209500 chr7D 169420739 169422988 2249 True 1396.50 1520 90.647000 597 2788 2 chr7D.!!$R3 2191
14 TraesCS7A01G209500 chr7D 169539863 169540918 1055 True 1323.00 1323 89.775000 634 1663 1 chr7D.!!$R2 1029
15 TraesCS7A01G209500 chr7D 165118979 165119999 1020 False 1158.00 1158 87.228000 1730 2772 1 chr7D.!!$F1 1042
16 TraesCS7A01G209500 chr7D 164750884 164751904 1020 True 1103.00 1103 86.385000 1730 2773 1 chr7D.!!$R1 1043
17 TraesCS7A01G209500 chr7D 169025261 169026921 1660 False 1023.05 1949 89.787500 1687 3359 2 chr7D.!!$F4 1672
18 TraesCS7A01G209500 chr7D 168990533 168992070 1537 False 1009.50 1666 88.815000 566 2086 2 chr7D.!!$F3 1520
19 TraesCS7A01G209500 chr7D 184212085 184212631 546 False 324.00 324 77.897000 18 565 1 chr7D.!!$F2 547
20 TraesCS7A01G209500 chr6A 124422812 124425350 2538 False 1549.00 1849 89.682500 786 3319 2 chr6A.!!$F2 2533
21 TraesCS7A01G209500 chr6A 124916144 124917059 915 True 1238.00 1238 91.285000 786 1690 1 chr6A.!!$R1 904
22 TraesCS7A01G209500 chr6A 602963659 602964220 561 False 403.00 403 79.860000 1 565 1 chr6A.!!$F1 564
23 TraesCS7A01G209500 chrUn 218480268 218481232 964 False 1321.00 1321 91.322000 1808 2788 1 chrUn.!!$F1 980
24 TraesCS7A01G209500 chrUn 342996805 342997736 931 True 1277.00 1277 91.542000 739 1663 1 chrUn.!!$R1 924
25 TraesCS7A01G209500 chrUn 244606725 244607727 1002 False 1227.00 1227 88.889000 681 1690 1 chrUn.!!$F2 1009
26 TraesCS7A01G209500 chrUn 262505029 262507812 2783 False 1145.00 1633 89.066333 598 3265 3 chrUn.!!$F3 2667
27 TraesCS7A01G209500 chrUn 326638914 326640397 1483 False 962.00 1633 87.544500 1687 3265 2 chrUn.!!$F4 1578
28 TraesCS7A01G209500 chr6D 103083910 103084974 1064 False 1330.00 1330 89.119000 1687 2788 1 chr6D.!!$F2 1101
29 TraesCS7A01G209500 chr6D 103051553 103052555 1002 False 1216.00 1216 88.694000 681 1690 1 chr6D.!!$F1 1009
30 TraesCS7A01G209500 chr4D 484947882 484948444 562 True 754.00 754 90.877000 2747 3312 1 chr4D.!!$R1 565
31 TraesCS7A01G209500 chr4D 249283392 249283956 564 False 747.00 747 90.543000 2747 3313 1 chr4D.!!$F2 566
32 TraesCS7A01G209500 chr3A 699606314 699606912 598 True 377.50 527 95.116000 1 471 2 chr3A.!!$R2 470
33 TraesCS7A01G209500 chr3A 747742105 747742634 529 True 279.00 279 76.710000 15 542 1 chr3A.!!$R1 527
34 TraesCS7A01G209500 chr1A 551730938 551731499 561 False 409.00 409 80.070000 1 565 1 chr1A.!!$F1 564
35 TraesCS7A01G209500 chr5B 582903438 582904004 566 False 387.00 387 79.304000 1 565 1 chr5B.!!$F1 564
36 TraesCS7A01G209500 chr6B 129491842 129492404 562 False 344.00 344 77.972000 1 565 1 chr6B.!!$F1 564
37 TraesCS7A01G209500 chr3B 787400951 787401498 547 True 342.00 342 78.237000 17 565 1 chr3B.!!$R1 548
38 TraesCS7A01G209500 chr2A 773298445 773298991 546 True 329.00 329 78.075000 18 565 1 chr2A.!!$R1 547

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
439 583 0.111266 CGCGTCTCCGACAAAAACAG 60.111 55.0 0.0 0.0 35.63 3.16 F
1308 1539 0.253327 GGACCATCCAGAAGACCACC 59.747 60.0 0.0 0.0 36.28 4.61 F
1754 4141 0.105778 GCTCCTGAGATTTCCTCCCG 59.894 60.0 0.0 0.0 41.25 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 4141 0.322975 AGACTCCAGCACATGTGACC 59.677 55.000 29.8 12.58 0.00 4.02 R
2193 4641 0.694444 ACAAGTGGTCCTGTCCCTGT 60.694 55.000 0.0 0.00 0.00 4.00 R
2563 5030 1.003580 TCCATCACAGGAAACAGAGCC 59.996 52.381 0.0 0.00 33.93 4.70 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
384 522 6.238648 CGGACATACTAATTTTTGGTCCATCC 60.239 42.308 0.00 0.00 42.60 3.51
394 532 1.274703 TGGTCCATCCTGAGCCTTCC 61.275 60.000 0.00 0.00 37.07 3.46
439 583 0.111266 CGCGTCTCCGACAAAAACAG 60.111 55.000 0.00 0.00 35.63 3.16
498 642 2.203209 GAATCGCCGGGGCATTCT 60.203 61.111 23.80 6.81 42.06 2.40
553 697 2.835705 CGTCCGGTCATCCTCCTCG 61.836 68.421 0.00 0.00 0.00 4.63
554 698 1.753463 GTCCGGTCATCCTCCTCGT 60.753 63.158 0.00 0.00 0.00 4.18
567 711 2.105128 CTCGTGGGAGGACGCATC 59.895 66.667 0.00 0.00 40.82 3.91
568 712 2.678580 TCGTGGGAGGACGCATCA 60.679 61.111 0.00 0.00 40.82 3.07
569 713 2.509336 CGTGGGAGGACGCATCAC 60.509 66.667 0.00 0.00 40.82 3.06
614 758 2.747467 CGACTAAGGTCCGAGGGTATGA 60.747 54.545 0.00 0.00 39.15 2.15
649 798 3.939592 GACCCGGAAAAGAATAGGACTTG 59.060 47.826 0.73 0.00 0.00 3.16
650 799 3.329814 ACCCGGAAAAGAATAGGACTTGT 59.670 43.478 0.73 0.00 0.00 3.16
651 800 4.533311 ACCCGGAAAAGAATAGGACTTGTA 59.467 41.667 0.73 0.00 0.00 2.41
733 882 1.136141 GCATCATGATCGGATTGACGC 60.136 52.381 4.86 0.00 0.00 5.19
801 973 1.070134 CTGACGGGAAACTGAACTGGA 59.930 52.381 0.00 0.00 41.09 3.86
802 974 1.202604 TGACGGGAAACTGAACTGGAC 60.203 52.381 0.00 0.00 41.09 4.02
829 1003 8.432805 ACATAGTCGGATTCAGATAAGGAAATT 58.567 33.333 0.00 0.00 0.00 1.82
830 1004 8.715998 CATAGTCGGATTCAGATAAGGAAATTG 58.284 37.037 0.00 0.00 0.00 2.32
869 1049 4.778154 GCGTAGTGCAGCGTCTTTAAATAC 60.778 45.833 7.03 0.00 45.45 1.89
882 1066 5.472137 GTCTTTAAATACCAGCACAGACCAA 59.528 40.000 0.00 0.00 0.00 3.67
884 1068 2.200373 AATACCAGCACAGACCAACC 57.800 50.000 0.00 0.00 0.00 3.77
914 1105 1.916777 AACACCTTCCCGATCCCGT 60.917 57.895 0.00 0.00 0.00 5.28
1308 1539 0.253327 GGACCATCCAGAAGACCACC 59.747 60.000 0.00 0.00 36.28 4.61
1335 1566 2.738521 CACGCGGGAGTCAAGGTG 60.739 66.667 12.47 0.00 0.00 4.00
1371 1602 3.716872 ACCTGTCTTTCAAGAAGAAGGGA 59.283 43.478 14.37 0.00 37.01 4.20
1380 1611 3.716872 TCAAGAAGAAGGGAAAGTCCACT 59.283 43.478 0.00 0.00 38.64 4.00
1536 1767 1.900498 GCAACAGCAACCAGAGGCT 60.900 57.895 0.00 0.00 42.06 4.58
1546 1777 3.314331 CAGAGGCTGTGACCCCGT 61.314 66.667 5.59 0.00 0.00 5.28
1679 3985 5.352284 GTCGTTCTTGATGTATGATGAGGT 58.648 41.667 0.00 0.00 0.00 3.85
1709 4066 2.509166 TCATCCGAGTCCACTACAGT 57.491 50.000 0.00 0.00 0.00 3.55
1754 4141 0.105778 GCTCCTGAGATTTCCTCCCG 59.894 60.000 0.00 0.00 41.25 5.14
1972 4417 2.500229 TGGAAGACGACCCAATTGAAC 58.500 47.619 7.12 0.00 0.00 3.18
1988 4433 1.344438 TGAACTTGAGCCGATCACTGT 59.656 47.619 0.00 0.00 37.77 3.55
2148 4593 2.029623 GCCTTCCATGATGCTGACAAT 58.970 47.619 0.00 0.00 0.00 2.71
2166 4611 5.171339 ACAATGAGAAGAGGTACAATGCT 57.829 39.130 0.00 0.00 0.00 3.79
2193 4641 1.001268 GATCTTGACGCTCCATCGCTA 60.001 52.381 0.00 0.00 0.00 4.26
2372 4829 8.197988 AGTGTCTATTAAATCCGATGTTGAAC 57.802 34.615 0.00 0.00 0.00 3.18
2513 4979 2.687935 TGTTGTTGTTCTTCTTGCTCCC 59.312 45.455 0.00 0.00 0.00 4.30
2538 5005 4.022068 TGATGGATTTTCTGAACCTTGCAC 60.022 41.667 0.00 0.00 0.00 4.57
2563 5030 1.272490 TCCTGCACCAGTACTTCTTCG 59.728 52.381 0.00 0.00 0.00 3.79
2605 5087 6.719370 TGGACCATGTTAAAACTGCTCTTATT 59.281 34.615 0.00 0.00 0.00 1.40
2883 5408 7.540055 CCTTGAAATCTAAGTGCAATTTGTCTC 59.460 37.037 4.05 2.90 0.00 3.36
2885 5410 8.846943 TGAAATCTAAGTGCAATTTGTCTCTA 57.153 30.769 4.05 0.00 0.00 2.43
2886 5411 8.721478 TGAAATCTAAGTGCAATTTGTCTCTAC 58.279 33.333 4.05 0.00 0.00 2.59
2887 5412 8.621532 AAATCTAAGTGCAATTTGTCTCTACA 57.378 30.769 4.05 0.00 0.00 2.74
2888 5413 8.621532 AATCTAAGTGCAATTTGTCTCTACAA 57.378 30.769 4.05 0.00 43.85 2.41
2899 5426 8.725148 CAATTTGTCTCTACAAGCTAACTGAAT 58.275 33.333 0.00 0.00 45.99 2.57
3000 5531 6.127897 ACAGTGCCTTGATCTAAAATAGTTGC 60.128 38.462 0.00 0.00 0.00 4.17
3030 5563 9.595823 TTAGCTCCATAGTTCTGTGTAATTTAC 57.404 33.333 0.00 0.00 0.00 2.01
3124 5658 7.605691 ACAGGAAGAACATGAGACTAAATTGAG 59.394 37.037 0.00 0.00 34.19 3.02
3268 5808 5.122396 GTGATCTGAACAGGTTTATGTGACC 59.878 44.000 1.93 0.00 37.44 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
278 416 6.464465 GGTTCATAGGCTTGCTTTAGATCCTA 60.464 42.308 0.00 0.00 0.00 2.94
279 417 5.372373 GTTCATAGGCTTGCTTTAGATCCT 58.628 41.667 0.00 0.00 0.00 3.24
327 465 7.398904 TGGGAGGAAAGGAGGTTTAATTTATTG 59.601 37.037 0.00 0.00 0.00 1.90
328 466 7.483881 TGGGAGGAAAGGAGGTTTAATTTATT 58.516 34.615 0.00 0.00 0.00 1.40
329 467 7.051696 TGGGAGGAAAGGAGGTTTAATTTAT 57.948 36.000 0.00 0.00 0.00 1.40
330 468 6.471942 TGGGAGGAAAGGAGGTTTAATTTA 57.528 37.500 0.00 0.00 0.00 1.40
331 469 5.348259 TGGGAGGAAAGGAGGTTTAATTT 57.652 39.130 0.00 0.00 0.00 1.82
334 472 3.920197 TGATGGGAGGAAAGGAGGTTTAA 59.080 43.478 0.00 0.00 0.00 1.52
394 532 1.291184 TTCGGCTGAATGTCTGCGTG 61.291 55.000 3.13 0.00 41.49 5.34
498 642 1.003118 CTGGAATTGTCGGGGACTTGA 59.997 52.381 0.00 0.00 33.15 3.02
553 697 2.509336 CGTGATGCGTCCTCCCAC 60.509 66.667 2.83 0.00 35.54 4.61
554 698 4.451150 GCGTGATGCGTCCTCCCA 62.451 66.667 2.83 0.00 43.66 4.37
565 709 5.345702 CATTTCTTTTCATCCATGCGTGAT 58.654 37.500 7.72 0.00 0.00 3.06
566 710 4.380761 CCATTTCTTTTCATCCATGCGTGA 60.381 41.667 7.72 0.00 0.00 4.35
567 711 3.861113 CCATTTCTTTTCATCCATGCGTG 59.139 43.478 0.00 0.00 0.00 5.34
568 712 3.763360 TCCATTTCTTTTCATCCATGCGT 59.237 39.130 0.00 0.00 0.00 5.24
569 713 4.374843 TCCATTTCTTTTCATCCATGCG 57.625 40.909 0.00 0.00 0.00 4.73
570 714 5.295152 GGATCCATTTCTTTTCATCCATGC 58.705 41.667 6.95 0.00 31.68 4.06
571 715 5.300034 TCGGATCCATTTCTTTTCATCCATG 59.700 40.000 13.41 0.00 31.68 3.66
614 758 6.439058 TCTTTTCCGGGTCCATTTATTTGAAT 59.561 34.615 0.00 0.00 0.00 2.57
649 798 8.880750 GTGATTCTTGATTTTGGGTAGTACTAC 58.119 37.037 22.53 22.53 35.40 2.73
650 799 8.598916 TGTGATTCTTGATTTTGGGTAGTACTA 58.401 33.333 0.00 0.00 0.00 1.82
651 800 7.458397 TGTGATTCTTGATTTTGGGTAGTACT 58.542 34.615 0.00 0.00 0.00 2.73
801 973 5.833667 TCCTTATCTGAATCCGACTATGTGT 59.166 40.000 0.00 0.00 0.00 3.72
802 974 6.332735 TCCTTATCTGAATCCGACTATGTG 57.667 41.667 0.00 0.00 0.00 3.21
869 1049 3.357079 GCGGTTGGTCTGTGCTGG 61.357 66.667 0.00 0.00 0.00 4.85
882 1066 4.588854 TGTTGTGGTACGCGCGGT 62.589 61.111 35.22 21.38 45.01 5.68
884 1068 4.067016 GGTGTTGTGGTACGCGCG 62.067 66.667 30.96 30.96 45.01 6.86
914 1105 3.265995 GGGATTTGGGAGAGGTTTGTCTA 59.734 47.826 0.00 0.00 0.00 2.59
1308 1539 3.864686 CCCGCGTGGCAAATCTCG 61.865 66.667 10.27 0.00 0.00 4.04
1356 1587 4.887655 GTGGACTTTCCCTTCTTCTTGAAA 59.112 41.667 0.00 0.00 35.03 2.69
1380 1611 0.920763 ATTCCTCCATGACCCAGCCA 60.921 55.000 0.00 0.00 0.00 4.75
1440 1671 2.342910 GCATTCTGCAGAACACCTTG 57.657 50.000 30.66 23.75 44.26 3.61
1608 1839 2.279784 CCGCGCATCCTCTTCTCC 60.280 66.667 8.75 0.00 0.00 3.71
1609 1840 1.880340 CACCGCGCATCCTCTTCTC 60.880 63.158 8.75 0.00 0.00 2.87
1679 3985 0.964700 CTCGGATGATGCTCTGGCTA 59.035 55.000 0.00 0.00 39.59 3.93
1709 4066 2.611971 GCAACGTCAGAGTGGTTGGATA 60.612 50.000 9.72 0.00 40.93 2.59
1754 4141 0.322975 AGACTCCAGCACATGTGACC 59.677 55.000 29.80 12.58 0.00 4.02
1806 4244 1.748122 AATGCTTGAGCCAGCCTCG 60.748 57.895 0.00 0.00 43.82 4.63
1972 4417 1.565305 GCTACAGTGATCGGCTCAAG 58.435 55.000 0.00 0.00 35.07 3.02
2002 4447 0.920763 TCCTGTTGGCCCATCTCCAT 60.921 55.000 0.00 0.00 32.92 3.41
2148 4593 2.675032 CGCAGCATTGTACCTCTTCTCA 60.675 50.000 0.00 0.00 0.00 3.27
2193 4641 0.694444 ACAAGTGGTCCTGTCCCTGT 60.694 55.000 0.00 0.00 0.00 4.00
2372 4829 6.395629 TCCTCGTATACACTTTGAAAAGAGG 58.604 40.000 9.71 6.72 41.92 3.69
2513 4979 4.726416 CAAGGTTCAGAAAATCCATCACG 58.274 43.478 0.00 0.00 0.00 4.35
2538 5005 1.153745 GTACTGGTGCAGGAGCGAG 60.154 63.158 0.00 0.00 46.23 5.03
2563 5030 1.003580 TCCATCACAGGAAACAGAGCC 59.996 52.381 0.00 0.00 33.93 4.70
2605 5087 9.855021 GCTTATCTGAGCCTAATAAAACAAAAA 57.145 29.630 0.00 0.00 36.66 1.94
2610 5092 6.484977 AGCTGCTTATCTGAGCCTAATAAAAC 59.515 38.462 0.00 0.00 42.01 2.43
2611 5093 6.595682 AGCTGCTTATCTGAGCCTAATAAAA 58.404 36.000 0.00 0.00 42.01 1.52
2613 5095 5.815233 AGCTGCTTATCTGAGCCTAATAA 57.185 39.130 0.00 0.00 42.01 1.40
2652 5150 8.307582 ACGTAGTTACTCCTACTACTTACCTA 57.692 38.462 10.39 0.00 43.62 3.08
2793 5316 8.372459 TGACACTGTAATAACTGTTTACTCCAT 58.628 33.333 0.00 0.00 35.79 3.41
2885 5410 9.726438 AGATACTGTAAAATTCAGTTAGCTTGT 57.274 29.630 3.85 0.00 42.50 3.16
3000 5531 6.992063 ACACAGAACTATGGAGCTAAAATG 57.008 37.500 0.00 0.00 0.00 2.32
3124 5658 5.631119 ACATATAACATTGGAGGGTTAGGC 58.369 41.667 0.00 0.00 33.41 3.93


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

AutoCloner maintained by Alex Coulton.