Multiple sequence alignment - TraesCS5B01G037700

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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 TraesCS5B01G037700 chr5B 100.000 2168 0 0 1 2168 42159180 42157013 0.000000e+00 4004.0
1 TraesCS5B01G037700 chr5B 77.866 506 65 20 1180 1674 10267454 10266985 9.860000e-69 270.0
2 TraesCS5B01G037700 chr5B 82.008 239 18 8 1753 1967 10266977 10266740 1.710000e-41 180.0
3 TraesCS5B01G037700 chr5B 94.231 104 4 2 2022 2125 10266667 10266566 8.010000e-35 158.0
4 TraesCS5B01G037700 chr5A 87.492 1559 75 48 1 1494 8058130 8059633 0.000000e+00 1688.0
5 TraesCS5B01G037700 chr5A 82.184 174 10 10 1814 1967 8060803 8060975 1.750000e-26 130.0
6 TraesCS5B01G037700 chr5A 91.667 48 3 1 1701 1748 353601708 353601754 5.000000e-07 65.8
7 TraesCS5B01G037700 chr5D 90.420 762 38 18 614 1366 10037883 10038618 0.000000e+00 970.0
8 TraesCS5B01G037700 chr5D 91.054 313 12 5 204 514 10037166 10037464 2.000000e-110 409.0
9 TraesCS5B01G037700 chr5D 96.373 193 4 2 1 191 10036729 10036920 4.490000e-82 315.0
10 TraesCS5B01G037700 chr5D 83.590 195 18 5 1787 1967 10039300 10039494 1.030000e-38 171.0
11 TraesCS5B01G037700 chr5D 87.407 135 17 0 1504 1638 10038824 10038958 2.880000e-34 156.0
12 TraesCS5B01G037700 chr5D 90.385 104 8 2 2022 2125 10039563 10039664 3.750000e-28 135.0
13 TraesCS5B01G037700 chr6D 78.382 754 75 48 614 1343 382552434 382551745 2.000000e-110 409.0
14 TraesCS5B01G037700 chr6D 91.000 300 19 8 309 604 382552830 382552535 4.340000e-107 398.0
15 TraesCS5B01G037700 chr6D 100.000 34 0 0 1487 1520 21072736 21072703 1.800000e-06 63.9
16 TraesCS5B01G037700 chr6D 90.244 41 4 0 1701 1741 380137064 380137024 1.000000e-03 54.7
17 TraesCS5B01G037700 chr6B 80.379 581 60 29 772 1343 572092268 572091733 2.020000e-105 392.0
18 TraesCS5B01G037700 chr6B 90.594 202 14 4 1 198 572093654 572093454 1.650000e-66 263.0
19 TraesCS5B01G037700 chr6B 88.325 197 12 6 208 402 572093291 572093104 2.170000e-55 226.0
20 TraesCS5B01G037700 chr6A 81.567 434 35 13 204 604 524334011 524333590 1.250000e-82 316.0
21 TraesCS5B01G037700 chr6A 82.020 406 39 20 937 1332 524333197 524332816 4.490000e-82 315.0
22 TraesCS5B01G037700 chr1D 93.478 46 3 0 1698 1743 413584496 413584541 3.860000e-08 69.4
23 TraesCS5B01G037700 chr2A 93.023 43 3 0 1699 1741 716548991 716548949 1.800000e-06 63.9
24 TraesCS5B01G037700 chr2A 97.143 35 1 0 1714 1748 773033908 773033874 2.320000e-05 60.2
25 TraesCS5B01G037700 chr2D 94.737 38 2 0 1711 1748 647448997 647449034 2.320000e-05 60.2
26 TraesCS5B01G037700 chr2B 94.595 37 1 1 1713 1748 788628077 788628041 3.010000e-04 56.5
27 TraesCS5B01G037700 chr3B 90.244 41 4 0 1701 1741 823196882 823196842 1.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G037700 chr5B 42157013 42159180 2167 True 4004.000000 4004 100.000000 1 2168 1 chr5B.!!$R1 2167
1 TraesCS5B01G037700 chr5B 10266566 10267454 888 True 202.666667 270 84.701667 1180 2125 3 chr5B.!!$R2 945
2 TraesCS5B01G037700 chr5A 8058130 8060975 2845 False 909.000000 1688 84.838000 1 1967 2 chr5A.!!$F2 1966
3 TraesCS5B01G037700 chr5D 10036729 10039664 2935 False 359.333333 970 89.871500 1 2125 6 chr5D.!!$F1 2124
4 TraesCS5B01G037700 chr6D 382551745 382552830 1085 True 403.500000 409 84.691000 309 1343 2 chr6D.!!$R3 1034
5 TraesCS5B01G037700 chr6B 572091733 572093654 1921 True 293.666667 392 86.432667 1 1343 3 chr6B.!!$R1 1342
6 TraesCS5B01G037700 chr6A 524332816 524334011 1195 True 315.500000 316 81.793500 204 1332 2 chr6A.!!$R1 1128

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
444 1172 0.61868 TATCAGAGGTGGTGCTGGCT 60.619 55.0 0.0 0.0 33.05 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 4745 0.320946 GATCCCCGGTCGACACAAAA 60.321 55.0 18.91 0.0 0.0 2.44 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
78 88 9.118300 GATGAAGAATAGTGTTTTCCATCTGAT 57.882 33.333 0.00 0.00 0.00 2.90
191 204 4.408596 AGGTTGAAATGTGTTTTCCCATGT 59.591 37.500 0.00 0.00 42.63 3.21
211 456 6.089820 CCATGTTTGTGAATTGTTGCATCTAC 59.910 38.462 0.00 0.00 0.00 2.59
254 605 2.808543 GGTTTCATGAGCTTTCGTCAGT 59.191 45.455 0.00 0.00 0.00 3.41
413 1101 8.746530 CCCAATCCTATATTTGGAATCTCATTG 58.253 37.037 5.60 3.51 44.23 2.82
444 1172 0.618680 TATCAGAGGTGGTGCTGGCT 60.619 55.000 0.00 0.00 33.05 4.75
445 1173 0.618680 ATCAGAGGTGGTGCTGGCTA 60.619 55.000 0.00 0.00 33.05 3.93
517 1246 3.149196 CAAGTGGTCATGGTTGCTACTT 58.851 45.455 0.00 0.00 33.97 2.24
586 1319 1.132495 AGGGAAGTGTTAGGACAGGGT 60.132 52.381 0.00 0.00 36.20 4.34
597 1331 5.014123 TGTTAGGACAGGGTGATTTTCTCAT 59.986 40.000 0.00 0.00 35.97 2.90
598 1332 4.664688 AGGACAGGGTGATTTTCTCATT 57.335 40.909 0.00 0.00 35.97 2.57
599 1333 4.338879 AGGACAGGGTGATTTTCTCATTG 58.661 43.478 0.00 0.00 35.97 2.82
600 1334 3.119352 GGACAGGGTGATTTTCTCATTGC 60.119 47.826 0.00 0.00 35.97 3.56
730 1892 9.559732 TTCTATCTGTAATGACCAAACATATGG 57.440 33.333 7.80 0.00 46.38 2.74
747 1909 5.073691 ACATATGGGGGTGGAATCTAAAGAG 59.926 44.000 7.80 0.00 0.00 2.85
769 1931 9.775854 AAGAGATGAATCACTATTAGACAATGG 57.224 33.333 0.00 0.00 0.00 3.16
770 1932 7.877097 AGAGATGAATCACTATTAGACAATGGC 59.123 37.037 0.00 0.00 0.00 4.40
811 1974 4.642429 TCTGTACTTTCTTTCCTGGAAGC 58.358 43.478 9.42 0.00 0.00 3.86
821 1986 3.402628 TTCCTGGAAGCACTTCAGTAC 57.597 47.619 4.68 0.00 41.20 2.73
822 1987 2.609747 TCCTGGAAGCACTTCAGTACT 58.390 47.619 12.21 0.00 41.20 2.73
824 1989 4.157246 TCCTGGAAGCACTTCAGTACTAA 58.843 43.478 12.21 0.00 41.20 2.24
850 2015 8.761575 ATGTGTCATTTAGCTTTATTGTTTGG 57.238 30.769 0.00 0.00 0.00 3.28
851 2016 7.946207 TGTGTCATTTAGCTTTATTGTTTGGA 58.054 30.769 0.00 0.00 0.00 3.53
852 2017 8.584157 TGTGTCATTTAGCTTTATTGTTTGGAT 58.416 29.630 0.00 0.00 0.00 3.41
888 2053 1.675483 TGTGTTTCTGCCACATGACAC 59.325 47.619 0.00 1.03 37.88 3.67
927 2099 6.834451 TCCAGGTTTTTGTCTTACCATGTTTA 59.166 34.615 0.00 0.00 34.32 2.01
947 2120 8.864069 TGTTTATTTTACAAACATCCTGTGTG 57.136 30.769 0.00 0.00 41.32 3.82
1047 2223 1.271840 TAGTGGGAGTGGGATGTGGC 61.272 60.000 0.00 0.00 0.00 5.01
1056 2232 0.177836 TGGGATGTGGCGTCTATGTG 59.822 55.000 0.00 0.00 0.00 3.21
1172 2357 5.512082 CGAAGAAAGACGACGACTGATTATT 59.488 40.000 0.00 0.00 0.00 1.40
1173 2358 6.685828 CGAAGAAAGACGACGACTGATTATTA 59.314 38.462 0.00 0.00 0.00 0.98
1174 2359 7.376336 CGAAGAAAGACGACGACTGATTATTAT 59.624 37.037 0.00 0.00 0.00 1.28
1196 2382 2.267045 GCCCATGGCGAAAAGAAGT 58.733 52.632 6.09 0.00 39.62 3.01
1197 2383 1.459450 GCCCATGGCGAAAAGAAGTA 58.541 50.000 6.09 0.00 39.62 2.24
1198 2384 2.024414 GCCCATGGCGAAAAGAAGTAT 58.976 47.619 6.09 0.00 39.62 2.12
1199 2385 3.211045 GCCCATGGCGAAAAGAAGTATA 58.789 45.455 6.09 0.00 39.62 1.47
1200 2386 3.821033 GCCCATGGCGAAAAGAAGTATAT 59.179 43.478 6.09 0.00 39.62 0.86
1201 2387 5.001232 GCCCATGGCGAAAAGAAGTATATA 58.999 41.667 6.09 0.00 39.62 0.86
1245 2434 9.393249 GAAACATGATCTTCGTGAATGTTAAAA 57.607 29.630 0.00 0.00 39.80 1.52
1246 2435 8.955061 AACATGATCTTCGTGAATGTTAAAAG 57.045 30.769 0.00 0.00 39.13 2.27
1247 2436 7.530010 ACATGATCTTCGTGAATGTTAAAAGG 58.470 34.615 0.00 0.00 36.89 3.11
1332 2549 9.699410 TGTGGATCTTTATGATGAAAACCTTAT 57.301 29.630 0.00 0.00 35.14 1.73
1400 2638 1.065126 GCATCTTACCAAGAGTGCCCT 60.065 52.381 9.97 0.00 41.61 5.19
1409 2647 1.891150 CAAGAGTGCCCTGATTTGCTT 59.109 47.619 0.00 0.00 0.00 3.91
1410 2648 1.831580 AGAGTGCCCTGATTTGCTTC 58.168 50.000 0.00 0.00 0.00 3.86
1411 2649 0.813821 GAGTGCCCTGATTTGCTTCC 59.186 55.000 0.00 0.00 0.00 3.46
1412 2650 0.613012 AGTGCCCTGATTTGCTTCCC 60.613 55.000 0.00 0.00 0.00 3.97
1413 2651 0.613012 GTGCCCTGATTTGCTTCCCT 60.613 55.000 0.00 0.00 0.00 4.20
1414 2652 0.612732 TGCCCTGATTTGCTTCCCTG 60.613 55.000 0.00 0.00 0.00 4.45
1415 2653 0.323725 GCCCTGATTTGCTTCCCTGA 60.324 55.000 0.00 0.00 0.00 3.86
1416 2654 1.687368 GCCCTGATTTGCTTCCCTGAT 60.687 52.381 0.00 0.00 0.00 2.90
1417 2655 2.743553 CCCTGATTTGCTTCCCTGATT 58.256 47.619 0.00 0.00 0.00 2.57
1418 2656 3.102204 CCCTGATTTGCTTCCCTGATTT 58.898 45.455 0.00 0.00 0.00 2.17
1419 2657 3.118884 CCCTGATTTGCTTCCCTGATTTG 60.119 47.826 0.00 0.00 0.00 2.32
1420 2658 3.518590 CTGATTTGCTTCCCTGATTTGC 58.481 45.455 0.00 0.00 0.00 3.68
1421 2659 2.234414 TGATTTGCTTCCCTGATTTGCC 59.766 45.455 0.00 0.00 0.00 4.52
1439 2677 6.757897 TTTGCCATCTCTTTACTGGTTATG 57.242 37.500 0.00 0.00 32.42 1.90
1441 2679 6.252599 TGCCATCTCTTTACTGGTTATGAT 57.747 37.500 0.00 0.00 32.42 2.45
1443 2681 5.049129 GCCATCTCTTTACTGGTTATGATGC 60.049 44.000 0.00 0.00 32.42 3.91
1472 2794 1.798813 CCTAGTTCACGGTTTCAGCAC 59.201 52.381 0.00 0.00 0.00 4.40
1480 2802 3.003275 TCACGGTTTCAGCACAAATTCTC 59.997 43.478 0.00 0.00 0.00 2.87
1486 2808 1.202758 TCAGCACAAATTCTCACCGGT 60.203 47.619 0.00 0.00 0.00 5.28
1487 2809 1.608590 CAGCACAAATTCTCACCGGTT 59.391 47.619 2.97 0.00 0.00 4.44
1488 2810 1.608590 AGCACAAATTCTCACCGGTTG 59.391 47.619 2.97 0.28 0.00 3.77
1489 2811 1.930371 GCACAAATTCTCACCGGTTGC 60.930 52.381 2.97 5.13 0.00 4.17
1490 2812 1.336440 CACAAATTCTCACCGGTTGCA 59.664 47.619 2.97 0.00 0.00 4.08
1491 2813 1.608590 ACAAATTCTCACCGGTTGCAG 59.391 47.619 2.97 0.59 0.00 4.41
1492 2814 0.598065 AAATTCTCACCGGTTGCAGC 59.402 50.000 2.97 0.00 0.00 5.25
1493 2815 0.250901 AATTCTCACCGGTTGCAGCT 60.251 50.000 2.97 0.00 0.00 4.24
1494 2816 0.613260 ATTCTCACCGGTTGCAGCTA 59.387 50.000 2.97 0.00 0.00 3.32
1495 2817 0.613260 TTCTCACCGGTTGCAGCTAT 59.387 50.000 2.97 0.00 0.00 2.97
1496 2818 0.175760 TCTCACCGGTTGCAGCTATC 59.824 55.000 2.97 0.00 0.00 2.08
1497 2819 0.176680 CTCACCGGTTGCAGCTATCT 59.823 55.000 2.97 0.00 0.00 1.98
1498 2820 0.175760 TCACCGGTTGCAGCTATCTC 59.824 55.000 2.97 0.00 0.00 2.75
1499 2821 1.141881 ACCGGTTGCAGCTATCTCG 59.858 57.895 0.00 0.00 0.00 4.04
1500 2822 2.240500 CCGGTTGCAGCTATCTCGC 61.241 63.158 0.00 0.00 0.00 5.03
1501 2823 1.519234 CGGTTGCAGCTATCTCGCA 60.519 57.895 0.00 0.00 0.00 5.10
1502 2824 1.485838 CGGTTGCAGCTATCTCGCAG 61.486 60.000 0.00 0.00 36.91 5.18
1503 2825 1.640604 GTTGCAGCTATCTCGCAGC 59.359 57.895 0.00 0.00 42.02 5.25
1504 2826 1.522355 TTGCAGCTATCTCGCAGCC 60.522 57.895 0.00 0.00 41.12 4.85
1546 2868 4.373116 GTTGTCCGCCTCGCCTGA 62.373 66.667 0.00 0.00 0.00 3.86
1677 3010 3.263941 GGTTGACGATGGCGCTTT 58.736 55.556 7.64 0.00 42.48 3.51
1678 3011 1.154225 GGTTGACGATGGCGCTTTG 60.154 57.895 7.64 1.58 42.48 2.77
1679 3012 1.573829 GGTTGACGATGGCGCTTTGA 61.574 55.000 7.64 0.00 42.48 2.69
1680 3013 0.179215 GTTGACGATGGCGCTTTGAG 60.179 55.000 7.64 0.00 42.48 3.02
1681 3014 1.911293 TTGACGATGGCGCTTTGAGC 61.911 55.000 7.64 0.00 42.48 4.26
1683 3016 0.806102 GACGATGGCGCTTTGAGCTA 60.806 55.000 7.64 0.00 39.60 3.32
1684 3017 0.391130 ACGATGGCGCTTTGAGCTAA 60.391 50.000 7.64 0.00 39.60 3.09
1686 3019 1.331756 CGATGGCGCTTTGAGCTAAAT 59.668 47.619 7.64 0.00 39.60 1.40
1687 3020 2.600792 CGATGGCGCTTTGAGCTAAATC 60.601 50.000 7.64 0.00 39.60 2.17
1688 3021 1.094785 TGGCGCTTTGAGCTAAATCC 58.905 50.000 7.64 0.00 39.60 3.01
1702 3670 9.525409 TTGAGCTAAATCCGTAATTTCTACTAC 57.475 33.333 0.00 0.00 38.53 2.73
1704 3672 9.396938 GAGCTAAATCCGTAATTTCTACTACTC 57.603 37.037 0.00 0.00 38.53 2.59
1705 3673 8.358895 AGCTAAATCCGTAATTTCTACTACTCC 58.641 37.037 0.00 0.00 38.53 3.85
1706 3674 8.139989 GCTAAATCCGTAATTTCTACTACTCCA 58.860 37.037 0.00 0.00 38.53 3.86
1713 3681 8.131100 CCGTAATTTCTACTACTCCATTCGTTA 58.869 37.037 0.00 0.00 0.00 3.18
1724 3692 9.751542 ACTACTCCATTCGTTAAGAAATATGAG 57.248 33.333 0.00 0.00 42.91 2.90
1726 3694 8.879342 ACTCCATTCGTTAAGAAATATGAGAG 57.121 34.615 11.55 0.00 42.91 3.20
1727 3695 8.478877 ACTCCATTCGTTAAGAAATATGAGAGT 58.521 33.333 11.55 0.00 42.91 3.24
1728 3696 8.648557 TCCATTCGTTAAGAAATATGAGAGTG 57.351 34.615 0.00 0.00 42.91 3.51
1729 3697 8.258007 TCCATTCGTTAAGAAATATGAGAGTGT 58.742 33.333 0.00 0.00 42.91 3.55
1770 4041 7.772166 AGTCTCTTTTGGTAAAAGGTTTTGAG 58.228 34.615 12.53 4.15 46.11 3.02
1777 4048 5.187687 TGGTAAAAGGTTTTGAGTCTCGTT 58.812 37.500 0.00 0.00 0.00 3.85
1785 4056 2.512485 TTGAGTCTCGTTTTGCCGTA 57.488 45.000 0.00 0.00 0.00 4.02
1878 4427 2.428960 TACACGCGTGCATCACCACT 62.429 55.000 37.35 17.99 33.60 4.00
1879 4428 2.738521 ACGCGTGCATCACCACTC 60.739 61.111 12.93 0.00 33.60 3.51
1880 4429 3.490759 CGCGTGCATCACCACTCC 61.491 66.667 0.00 0.00 33.60 3.85
1958 4520 2.431683 GCACCTGCCAACCTCTGA 59.568 61.111 0.00 0.00 34.31 3.27
1959 4521 1.228245 GCACCTGCCAACCTCTGAA 60.228 57.895 0.00 0.00 34.31 3.02
1960 4522 0.610232 GCACCTGCCAACCTCTGAAT 60.610 55.000 0.00 0.00 34.31 2.57
1961 4523 1.457346 CACCTGCCAACCTCTGAATC 58.543 55.000 0.00 0.00 0.00 2.52
1962 4524 1.067295 ACCTGCCAACCTCTGAATCA 58.933 50.000 0.00 0.00 0.00 2.57
1963 4525 1.637553 ACCTGCCAACCTCTGAATCAT 59.362 47.619 0.00 0.00 0.00 2.45
1964 4526 2.042162 ACCTGCCAACCTCTGAATCATT 59.958 45.455 0.00 0.00 0.00 2.57
1965 4527 3.266772 ACCTGCCAACCTCTGAATCATTA 59.733 43.478 0.00 0.00 0.00 1.90
1966 4528 4.263905 ACCTGCCAACCTCTGAATCATTAA 60.264 41.667 0.00 0.00 0.00 1.40
1967 4529 4.337555 CCTGCCAACCTCTGAATCATTAAG 59.662 45.833 0.00 0.00 0.00 1.85
1968 4530 5.178096 TGCCAACCTCTGAATCATTAAGA 57.822 39.130 0.00 0.00 0.00 2.10
1969 4531 4.943705 TGCCAACCTCTGAATCATTAAGAC 59.056 41.667 0.00 0.00 0.00 3.01
1970 4532 4.336713 GCCAACCTCTGAATCATTAAGACC 59.663 45.833 0.00 0.00 0.00 3.85
1971 4533 5.749462 CCAACCTCTGAATCATTAAGACCT 58.251 41.667 0.00 0.00 0.00 3.85
1972 4534 5.819901 CCAACCTCTGAATCATTAAGACCTC 59.180 44.000 0.00 0.00 0.00 3.85
1973 4535 6.409704 CAACCTCTGAATCATTAAGACCTCA 58.590 40.000 0.00 0.00 0.00 3.86
1974 4536 6.627087 ACCTCTGAATCATTAAGACCTCAA 57.373 37.500 0.00 0.00 0.00 3.02
1975 4537 7.020827 ACCTCTGAATCATTAAGACCTCAAA 57.979 36.000 0.00 0.00 0.00 2.69
1976 4538 7.461749 ACCTCTGAATCATTAAGACCTCAAAA 58.538 34.615 0.00 0.00 0.00 2.44
1977 4539 8.112183 ACCTCTGAATCATTAAGACCTCAAAAT 58.888 33.333 0.00 0.00 0.00 1.82
1978 4540 9.618890 CCTCTGAATCATTAAGACCTCAAAATA 57.381 33.333 0.00 0.00 0.00 1.40
2082 4701 1.731969 GTACCACGTGTCGGCTCAC 60.732 63.158 15.65 0.00 35.28 3.51
2092 4711 1.474478 TGTCGGCTCACTCTGATTCTC 59.526 52.381 0.00 0.00 0.00 2.87
2100 4719 4.274459 GCTCACTCTGATTCTCTCTCTCTC 59.726 50.000 0.00 0.00 0.00 3.20
2101 4720 4.780815 TCACTCTGATTCTCTCTCTCTCC 58.219 47.826 0.00 0.00 0.00 3.71
2102 4721 3.561310 CACTCTGATTCTCTCTCTCTCCG 59.439 52.174 0.00 0.00 0.00 4.63
2103 4722 2.549754 CTCTGATTCTCTCTCTCTCCGC 59.450 54.545 0.00 0.00 0.00 5.54
2125 4744 4.551217 GCAAACGTATGTGAGTCACGAAAA 60.551 41.667 18.17 0.97 38.96 2.29
2126 4745 5.675970 CAAACGTATGTGAGTCACGAAAAT 58.324 37.500 18.17 8.69 38.96 1.82
2127 4746 5.917541 AACGTATGTGAGTCACGAAAATT 57.082 34.783 18.17 7.32 38.96 1.82
2128 4747 5.917541 ACGTATGTGAGTCACGAAAATTT 57.082 34.783 18.17 0.00 38.96 1.82
2129 4748 6.295039 ACGTATGTGAGTCACGAAAATTTT 57.705 33.333 18.17 2.28 38.96 1.82
2130 4749 6.133392 ACGTATGTGAGTCACGAAAATTTTG 58.867 36.000 18.17 3.68 38.96 2.44
2131 4750 6.133392 CGTATGTGAGTCACGAAAATTTTGT 58.867 36.000 18.17 4.31 37.89 2.83
2132 4751 6.084939 CGTATGTGAGTCACGAAAATTTTGTG 59.915 38.462 17.67 17.67 37.89 3.33
2133 4752 5.303747 TGTGAGTCACGAAAATTTTGTGT 57.696 34.783 21.52 13.33 37.14 3.72
2134 4753 5.328691 TGTGAGTCACGAAAATTTTGTGTC 58.671 37.500 21.52 17.26 37.14 3.67
2135 4754 4.433304 GTGAGTCACGAAAATTTTGTGTCG 59.567 41.667 21.52 16.29 39.37 4.35
2136 4755 4.330347 TGAGTCACGAAAATTTTGTGTCGA 59.670 37.500 21.52 9.08 36.98 4.20
2137 4756 4.584394 AGTCACGAAAATTTTGTGTCGAC 58.416 39.130 21.52 9.11 36.98 4.20
2138 4757 3.722289 GTCACGAAAATTTTGTGTCGACC 59.278 43.478 21.52 5.06 36.98 4.79
2139 4758 2.711964 CACGAAAATTTTGTGTCGACCG 59.288 45.455 14.12 7.51 36.98 4.79
2140 4759 2.286536 ACGAAAATTTTGTGTCGACCGG 60.287 45.455 14.12 0.00 36.98 5.28
2141 4760 2.657184 GAAAATTTTGTGTCGACCGGG 58.343 47.619 14.12 0.00 0.00 5.73
2142 4761 0.955905 AAATTTTGTGTCGACCGGGG 59.044 50.000 14.12 0.00 0.00 5.73
2143 4762 0.108963 AATTTTGTGTCGACCGGGGA 59.891 50.000 14.12 0.00 0.00 4.81
2144 4763 0.326927 ATTTTGTGTCGACCGGGGAT 59.673 50.000 14.12 0.00 0.00 3.85
2145 4764 0.320946 TTTTGTGTCGACCGGGGATC 60.321 55.000 14.12 0.00 0.00 3.36
2146 4765 2.175035 TTTGTGTCGACCGGGGATCC 62.175 60.000 14.12 1.92 0.00 3.36
2147 4766 3.072468 GTGTCGACCGGGGATCCA 61.072 66.667 15.23 0.00 0.00 3.41
2148 4767 2.042333 TGTCGACCGGGGATCCAT 60.042 61.111 15.23 0.00 0.00 3.41
2149 4768 1.687840 TGTCGACCGGGGATCCATT 60.688 57.895 15.23 0.00 0.00 3.16
2150 4769 1.069258 GTCGACCGGGGATCCATTC 59.931 63.158 15.23 2.64 0.00 2.67
2151 4770 2.029073 CGACCGGGGATCCATTCG 59.971 66.667 15.23 13.61 32.77 3.34
2152 4771 2.280865 GACCGGGGATCCATTCGC 60.281 66.667 15.23 0.00 36.58 4.70
2153 4772 2.768344 ACCGGGGATCCATTCGCT 60.768 61.111 15.23 0.00 37.45 4.93
2154 4773 2.031163 CCGGGGATCCATTCGCTC 59.969 66.667 15.23 0.00 37.45 5.03
2155 4774 2.356313 CGGGGATCCATTCGCTCG 60.356 66.667 15.23 1.71 37.45 5.03
2156 4775 2.666526 GGGGATCCATTCGCTCGC 60.667 66.667 15.23 0.00 37.45 5.03
2157 4776 3.038417 GGGATCCATTCGCTCGCG 61.038 66.667 15.23 0.00 41.35 5.87
2158 4777 3.038417 GGATCCATTCGCTCGCGG 61.038 66.667 6.95 0.00 40.25 6.46
2159 4778 2.027605 GATCCATTCGCTCGCGGA 59.972 61.111 6.13 2.46 40.25 5.54
2160 4779 2.279517 ATCCATTCGCTCGCGGAC 60.280 61.111 6.13 0.00 40.25 4.79
2161 4780 3.792053 ATCCATTCGCTCGCGGACC 62.792 63.158 6.13 0.00 40.25 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 204 4.023279 AGCGTAGATGCAACAATTCACAAA 60.023 37.500 0.00 0.00 37.31 2.83
211 456 3.745332 TGCATACTCATTTGTCAAGCG 57.255 42.857 0.00 0.00 0.00 4.68
287 640 5.470777 CCAATCAGCCAACAATTTCATTTGT 59.529 36.000 0.00 0.00 41.49 2.83
413 1101 3.325135 CACCTCTGATATTACTGACCCCC 59.675 52.174 0.00 0.00 0.00 5.40
517 1246 7.181305 TGTCACCTTCCAAGAATACCATACTAA 59.819 37.037 0.00 0.00 0.00 2.24
586 1319 4.039488 ACCAAGCAAGCAATGAGAAAATCA 59.961 37.500 0.00 0.00 43.70 2.57
597 1331 4.261801 GAGAGGTTATACCAAGCAAGCAA 58.738 43.478 0.00 0.00 41.95 3.91
598 1332 3.370527 GGAGAGGTTATACCAAGCAAGCA 60.371 47.826 0.00 0.00 41.95 3.91
599 1333 3.118223 AGGAGAGGTTATACCAAGCAAGC 60.118 47.826 0.00 0.00 41.95 4.01
600 1334 4.080863 ACAGGAGAGGTTATACCAAGCAAG 60.081 45.833 0.00 0.00 41.95 4.01
667 1811 5.464722 CGCTCAGTTGCTTCATATAGATTGT 59.535 40.000 0.00 0.00 0.00 2.71
730 1892 5.373812 TTCATCTCTTTAGATTCCACCCC 57.626 43.478 0.00 0.00 40.65 4.95
747 1909 7.734924 TGCCATTGTCTAATAGTGATTCATC 57.265 36.000 0.00 0.00 0.00 2.92
762 1924 2.731968 CGTTTACTGCCATGCCATTGTC 60.732 50.000 0.00 0.00 0.00 3.18
766 1928 2.288666 CTACGTTTACTGCCATGCCAT 58.711 47.619 0.00 0.00 0.00 4.40
767 1929 1.732941 CTACGTTTACTGCCATGCCA 58.267 50.000 0.00 0.00 0.00 4.92
768 1930 0.377203 GCTACGTTTACTGCCATGCC 59.623 55.000 0.00 0.00 0.00 4.40
769 1931 1.369625 AGCTACGTTTACTGCCATGC 58.630 50.000 0.00 0.00 0.00 4.06
770 1932 3.062639 CAGAAGCTACGTTTACTGCCATG 59.937 47.826 0.00 0.00 0.00 3.66
824 1989 9.206870 CCAAACAATAAAGCTAAATGACACATT 57.793 29.630 0.00 0.00 0.00 2.71
844 2009 9.524496 ACACTACTATATCGGTATATCCAAACA 57.476 33.333 0.00 0.00 35.57 2.83
845 2010 9.784680 CACACTACTATATCGGTATATCCAAAC 57.215 37.037 0.00 0.00 35.57 2.93
848 2013 9.524496 AAACACACTACTATATCGGTATATCCA 57.476 33.333 0.00 0.00 35.57 3.41
852 2017 8.509690 GCAGAAACACACTACTATATCGGTATA 58.490 37.037 0.00 0.00 0.00 1.47
853 2018 7.368833 GCAGAAACACACTACTATATCGGTAT 58.631 38.462 0.00 0.00 0.00 2.73
854 2019 6.238842 GGCAGAAACACACTACTATATCGGTA 60.239 42.308 0.00 0.00 0.00 4.02
855 2020 5.451520 GGCAGAAACACACTACTATATCGGT 60.452 44.000 0.00 0.00 0.00 4.69
856 2021 4.982916 GGCAGAAACACACTACTATATCGG 59.017 45.833 0.00 0.00 0.00 4.18
857 2022 5.459107 GTGGCAGAAACACACTACTATATCG 59.541 44.000 0.00 0.00 38.67 2.92
888 2053 8.576442 ACAAAAACCTGGAGTACAAATGATTAG 58.424 33.333 0.00 0.00 0.00 1.73
947 2120 3.320826 GGGGGTTATGTACATGCATTTCC 59.679 47.826 18.81 11.31 0.00 3.13
1047 2223 2.949451 AGTTCTGAGCCACATAGACG 57.051 50.000 0.00 0.00 0.00 4.18
1056 2232 2.067013 GGAACGTTGTAGTTCTGAGCC 58.933 52.381 5.00 0.00 46.99 4.70
1134 2310 1.875364 CTTCGGCGGCTTACGGTAC 60.875 63.158 7.21 0.00 44.51 3.34
1201 2387 8.753133 TCATGTTTCTGTCAAGTCAGAGTATAT 58.247 33.333 0.00 0.00 43.85 0.86
1400 2638 2.234414 GGCAAATCAGGGAAGCAAATCA 59.766 45.455 0.00 0.00 0.00 2.57
1409 2647 3.744940 AAAGAGATGGCAAATCAGGGA 57.255 42.857 0.00 0.00 0.00 4.20
1410 2648 4.337555 CAGTAAAGAGATGGCAAATCAGGG 59.662 45.833 0.00 0.00 0.00 4.45
1411 2649 4.337555 CCAGTAAAGAGATGGCAAATCAGG 59.662 45.833 0.00 0.00 0.00 3.86
1412 2650 4.946157 ACCAGTAAAGAGATGGCAAATCAG 59.054 41.667 0.00 0.00 37.64 2.90
1413 2651 4.922206 ACCAGTAAAGAGATGGCAAATCA 58.078 39.130 0.00 0.00 37.64 2.57
1414 2652 5.904362 AACCAGTAAAGAGATGGCAAATC 57.096 39.130 0.00 0.00 37.64 2.17
1415 2653 7.118723 TCATAACCAGTAAAGAGATGGCAAAT 58.881 34.615 0.00 0.00 37.64 2.32
1416 2654 6.480763 TCATAACCAGTAAAGAGATGGCAAA 58.519 36.000 0.00 0.00 37.64 3.68
1417 2655 6.061022 TCATAACCAGTAAAGAGATGGCAA 57.939 37.500 0.00 0.00 37.64 4.52
1418 2656 5.692115 TCATAACCAGTAAAGAGATGGCA 57.308 39.130 0.00 0.00 37.64 4.92
1419 2657 5.049129 GCATCATAACCAGTAAAGAGATGGC 60.049 44.000 0.00 0.00 37.64 4.40
1420 2658 6.057533 TGCATCATAACCAGTAAAGAGATGG 58.942 40.000 0.00 0.00 40.10 3.51
1421 2659 6.765036 ACTGCATCATAACCAGTAAAGAGATG 59.235 38.462 0.00 0.00 38.00 2.90
1461 2783 3.300009 GTGAGAATTTGTGCTGAAACCG 58.700 45.455 0.00 0.00 0.00 4.44
1472 2794 1.666888 GCTGCAACCGGTGAGAATTTG 60.667 52.381 8.52 0.75 0.00 2.32
1480 2802 1.148157 CGAGATAGCTGCAACCGGTG 61.148 60.000 8.52 3.35 0.00 4.94
1489 2811 2.355599 CCGGCTGCGAGATAGCTG 60.356 66.667 0.00 0.00 45.08 4.24
1490 2812 2.427245 AACCGGCTGCGAGATAGCT 61.427 57.895 0.00 0.00 40.92 3.32
1491 2813 2.107141 AACCGGCTGCGAGATAGC 59.893 61.111 0.00 0.00 40.41 2.97
1492 2814 2.240500 GCAACCGGCTGCGAGATAG 61.241 63.158 15.11 0.00 40.25 2.08
1493 2815 2.202878 GCAACCGGCTGCGAGATA 60.203 61.111 15.11 0.00 40.25 1.98
1494 2816 4.393155 TGCAACCGGCTGCGAGAT 62.393 61.111 23.90 0.00 45.74 2.75
1502 2824 2.597713 GCAAAAAGCTGCAACCGGC 61.598 57.895 0.00 0.00 42.17 6.13
1503 2825 2.302230 CGCAAAAAGCTGCAACCGG 61.302 57.895 0.00 0.00 42.77 5.28
1504 2826 2.302230 CCGCAAAAAGCTGCAACCG 61.302 57.895 1.02 0.00 42.77 4.44
1530 2852 2.852495 GAATCAGGCGAGGCGGACAA 62.852 60.000 1.32 0.00 0.00 3.18
1572 2894 8.965819 TGCCTGAAAATATGTAAATAAGCTTCA 58.034 29.630 0.00 0.00 0.00 3.02
1573 2895 9.237846 GTGCCTGAAAATATGTAAATAAGCTTC 57.762 33.333 0.00 0.00 0.00 3.86
1606 2928 8.674607 ACCCGTTCATATACATTTCTTTCTTTC 58.325 33.333 0.00 0.00 0.00 2.62
1613 2935 5.123227 CCACACCCGTTCATATACATTTCT 58.877 41.667 0.00 0.00 0.00 2.52
1659 2992 2.677003 AAAGCGCCATCGTCAACCG 61.677 57.895 2.29 0.00 38.14 4.44
1671 3004 5.955397 AAATTACGGATTTAGCTCAAAGCGC 60.955 40.000 0.00 0.00 37.12 5.92
1674 3007 9.099454 AGTAGAAATTACGGATTTAGCTCAAAG 57.901 33.333 0.00 0.00 38.06 2.77
1676 3009 9.525409 GTAGTAGAAATTACGGATTTAGCTCAA 57.475 33.333 0.00 0.00 38.06 3.02
1677 3010 8.910944 AGTAGTAGAAATTACGGATTTAGCTCA 58.089 33.333 0.00 0.00 38.06 4.26
1678 3011 9.396938 GAGTAGTAGAAATTACGGATTTAGCTC 57.603 37.037 0.00 0.00 38.06 4.09
1679 3012 8.358895 GGAGTAGTAGAAATTACGGATTTAGCT 58.641 37.037 0.00 0.00 38.06 3.32
1680 3013 8.139989 TGGAGTAGTAGAAATTACGGATTTAGC 58.860 37.037 0.00 0.00 38.06 3.09
1683 3016 9.543783 GAATGGAGTAGTAGAAATTACGGATTT 57.456 33.333 0.00 0.00 40.61 2.17
1684 3017 7.866393 CGAATGGAGTAGTAGAAATTACGGATT 59.134 37.037 0.00 0.00 0.00 3.01
1686 3019 6.319658 ACGAATGGAGTAGTAGAAATTACGGA 59.680 38.462 0.00 0.00 0.00 4.69
1687 3020 6.501781 ACGAATGGAGTAGTAGAAATTACGG 58.498 40.000 0.00 0.00 0.00 4.02
1688 3021 7.982371 AACGAATGGAGTAGTAGAAATTACG 57.018 36.000 0.00 0.00 0.00 3.18
1702 3670 8.759641 CACTCTCATATTTCTTAACGAATGGAG 58.240 37.037 0.00 0.00 0.00 3.86
1704 3672 8.425577 ACACTCTCATATTTCTTAACGAATGG 57.574 34.615 0.00 0.00 0.00 3.16
1750 3718 6.691388 CGAGACTCAAAACCTTTTACCAAAAG 59.309 38.462 2.82 4.72 45.78 2.27
1751 3719 6.151480 ACGAGACTCAAAACCTTTTACCAAAA 59.849 34.615 2.82 0.00 0.00 2.44
1752 3720 5.648960 ACGAGACTCAAAACCTTTTACCAAA 59.351 36.000 2.82 0.00 0.00 3.28
1757 4028 6.031471 GCAAAACGAGACTCAAAACCTTTTA 58.969 36.000 2.82 0.00 0.00 1.52
1758 4029 4.862574 GCAAAACGAGACTCAAAACCTTTT 59.137 37.500 2.82 0.00 0.00 2.27
1804 4080 5.596772 AGCCTGGTAAAAAGTACAAACACAT 59.403 36.000 0.00 0.00 0.00 3.21
1808 4084 4.581409 TGGAGCCTGGTAAAAAGTACAAAC 59.419 41.667 0.00 0.00 0.00 2.93
1811 4354 4.440826 TTGGAGCCTGGTAAAAAGTACA 57.559 40.909 0.00 0.00 0.00 2.90
1878 4427 1.533033 TCCGGAGAAGCACACAGGA 60.533 57.895 0.00 0.00 32.35 3.86
1879 4428 1.079543 CTCCGGAGAAGCACACAGG 60.080 63.158 28.21 0.00 0.00 4.00
1880 4429 1.079543 CCTCCGGAGAAGCACACAG 60.080 63.158 33.39 8.66 0.00 3.66
1983 4545 7.722363 ACAACTTTAATCATTCGGAGGTTTTT 58.278 30.769 0.00 0.00 0.00 1.94
1984 4546 7.284919 ACAACTTTAATCATTCGGAGGTTTT 57.715 32.000 0.00 0.00 0.00 2.43
1985 4547 6.894339 ACAACTTTAATCATTCGGAGGTTT 57.106 33.333 0.00 0.00 0.00 3.27
1986 4548 9.847224 ATATACAACTTTAATCATTCGGAGGTT 57.153 29.630 0.00 0.00 0.00 3.50
1987 4549 9.273016 CATATACAACTTTAATCATTCGGAGGT 57.727 33.333 0.00 0.00 0.00 3.85
1988 4550 8.230486 GCATATACAACTTTAATCATTCGGAGG 58.770 37.037 0.00 0.00 0.00 4.30
1989 4551 8.230486 GGCATATACAACTTTAATCATTCGGAG 58.770 37.037 0.00 0.00 0.00 4.63
1990 4552 7.095397 CGGCATATACAACTTTAATCATTCGGA 60.095 37.037 0.00 0.00 0.00 4.55
1991 4553 7.015289 CGGCATATACAACTTTAATCATTCGG 58.985 38.462 0.00 0.00 0.00 4.30
1992 4554 7.740346 GTCGGCATATACAACTTTAATCATTCG 59.260 37.037 0.00 0.00 0.00 3.34
1993 4555 7.740346 CGTCGGCATATACAACTTTAATCATTC 59.260 37.037 0.00 0.00 0.00 2.67
2076 4695 3.290710 AGAGAGAGAATCAGAGTGAGCC 58.709 50.000 0.00 0.00 37.82 4.70
2082 4701 2.549754 GCGGAGAGAGAGAGAATCAGAG 59.450 54.545 0.00 0.00 37.82 3.35
2092 4711 2.159366 ACATACGTTTGCGGAGAGAGAG 60.159 50.000 5.87 0.00 43.45 3.20
2100 4719 1.126113 GTGACTCACATACGTTTGCGG 59.874 52.381 5.87 0.00 37.05 5.69
2101 4720 1.201661 CGTGACTCACATACGTTTGCG 60.202 52.381 9.84 0.00 37.98 4.85
2102 4721 2.055838 TCGTGACTCACATACGTTTGC 58.944 47.619 9.84 0.00 38.80 3.68
2103 4722 4.702247 TTTCGTGACTCACATACGTTTG 57.298 40.909 9.84 4.33 38.80 2.93
2125 4744 0.326927 ATCCCCGGTCGACACAAAAT 59.673 50.000 18.91 2.03 0.00 1.82
2126 4745 0.320946 GATCCCCGGTCGACACAAAA 60.321 55.000 18.91 0.00 0.00 2.44
2127 4746 1.294138 GATCCCCGGTCGACACAAA 59.706 57.895 18.91 0.00 0.00 2.83
2128 4747 2.652095 GGATCCCCGGTCGACACAA 61.652 63.158 18.91 0.00 0.00 3.33
2129 4748 3.072468 GGATCCCCGGTCGACACA 61.072 66.667 18.91 0.00 0.00 3.72
2130 4749 1.968050 AATGGATCCCCGGTCGACAC 61.968 60.000 18.91 5.92 34.29 3.67
2131 4750 1.682451 GAATGGATCCCCGGTCGACA 61.682 60.000 18.91 0.00 34.29 4.35
2132 4751 1.069258 GAATGGATCCCCGGTCGAC 59.931 63.158 9.90 7.13 34.29 4.20
2133 4752 2.495409 CGAATGGATCCCCGGTCGA 61.495 63.158 9.90 0.00 41.28 4.20
2134 4753 2.029073 CGAATGGATCCCCGGTCG 59.971 66.667 9.90 9.03 35.80 4.79
2135 4754 2.280865 GCGAATGGATCCCCGGTC 60.281 66.667 9.90 0.12 34.29 4.79
2136 4755 2.768344 AGCGAATGGATCCCCGGT 60.768 61.111 9.90 12.76 34.29 5.28
2137 4756 2.031163 GAGCGAATGGATCCCCGG 59.969 66.667 9.90 0.00 34.29 5.73
2138 4757 2.356313 CGAGCGAATGGATCCCCG 60.356 66.667 9.90 11.35 34.29 5.73
2139 4758 2.666526 GCGAGCGAATGGATCCCC 60.667 66.667 9.90 0.00 0.00 4.81
2140 4759 3.038417 CGCGAGCGAATGGATCCC 61.038 66.667 12.58 0.00 42.83 3.85
2141 4760 3.038417 CCGCGAGCGAATGGATCC 61.038 66.667 19.72 4.20 42.83 3.36
2142 4761 2.027605 TCCGCGAGCGAATGGATC 59.972 61.111 19.72 0.00 42.83 3.36
2143 4762 2.279517 GTCCGCGAGCGAATGGAT 60.280 61.111 19.72 0.00 42.83 3.41
2144 4763 4.508128 GGTCCGCGAGCGAATGGA 62.508 66.667 19.72 4.54 42.83 3.41


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

AutoCloner maintained by Alex Coulton.